Contacts of the helix formed by residues 87 - 107 (chain A) in PDB entry 4IB4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LYS 4.8 2.0 - - - -
84A LYS* 3.2 33.3 - - - -
85A LEU* 2.9 10.6 + - - +
86A GLN* 1.3 77.7 - - - +
88A ALA* 1.3 55.4 + - - +
89A THR* 3.3 17.3 - - + -
90A ASN* 2.9 33.0 + - - +
91A TYR* 3.4 12.2 - - - -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 1.3 69.6 - - - +
89A THR* 1.3 61.0 + - - +
91A TYR* 3.2 32.0 + - - +
92A PHE* 4.0 3.0 + - - -
165A GLN 5.3 1.6 - - - +
168A SER* 3.5 44.6 - - - +
169A ARG* 3.9 7.6 - - + +
172A ALA* 3.5 16.7 - - + +
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Residues in contact with THR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 4.3 15.5 - - + -
88A ALA* 1.3 77.2 - - - +
90A ASN* 1.4 71.0 + - - +
92A PHE* 3.4 28.7 - - - +
93A LEU* 4.1 6.2 + - - +
149A ILE* 5.6 0.9 - - - +
152A ASP* 4.4 4.6 + - - -
153A ARG* 3.6 39.1 + - - +
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Residues in contact with ASN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 4.0 15.9 - - + +
85A LEU* 2.7 53.0 + - - +
87A TYR* 2.9 15.4 + - - +
89A THR* 1.4 81.7 + - - +
91A TYR* 1.4 60.8 + - - +
92A PHE 3.2 1.8 - - - -
93A LEU* 3.1 26.4 + - + +
94A MET* 3.0 25.1 + - - +
387A PHE* 3.7 13.3 - - - -
2010A PEG 3.9 7.6 + - - -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.2 21.1 - - + -
86A GLN* 3.7 31.7 + - - +
87A TYR 3.4 30.7 - - - -
88A ALA* 3.2 20.2 + - - +
90A ASN* 1.4 74.7 - - - +
92A PHE* 1.4 62.4 + - - +
94A MET* 3.8 15.7 - - + +
95A SER* 3.2 24.6 + - - -
169A ARG* 4.7 21.5 + - + -
172A ALA* 5.0 4.5 - - + -
173A PHE* 4.2 31.2 - + + -
176A ILE* 4.0 6.6 - - + +
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA 4.0 7.9 - - - -
89A THR* 3.4 22.4 + - - +
91A TYR* 1.4 78.2 - - - +
93A LEU* 1.4 56.5 + - + +
96A LEU* 3.2 26.9 + - - +
145A HIS* 3.5 11.6 - + - -
148A ALA* 3.9 24.0 - - + -
149A ILE* 3.8 30.4 - - + +
152A ASP* 3.7 29.2 - - + -
172A ALA* 4.0 23.3 - - + -
175A LYS* 3.7 42.0 - - + -
176A ILE* 3.6 21.5 - - + -
179A VAL* 6.0 0.2 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 4.2 12.3 - - + +
79A VAL* 5.1 0.4 - - + -
89A THR 4.4 6.1 - - - +
90A ASN* 3.1 35.3 + - - +
92A PHE* 1.4 77.3 - - + +
94A MET* 1.4 59.0 + - - +
96A LEU* 3.4 14.1 + - + +
97A ALA* 2.9 30.1 + - - +
149A ILE* 4.5 15.0 - - + -
377A PRO* 4.8 5.6 - - + +
380A TYR* 3.6 31.4 - - + -
381A THR* 4.1 9.6 - - + -
387A PHE* 3.9 21.5 - - + -
2010A PEG 4.0 15.5 - - - -
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Residues in contact with MET 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 5.2 1.3 - - - -
76A ILE* 4.0 26.7 - - + -
79A VAL* 4.0 32.0 - - + +
80A SER* 3.4 24.2 - - - +
90A ASN 3.0 14.7 + - - +
91A TYR* 3.8 18.4 - - + +
92A PHE 3.4 0.2 - - - -
93A LEU* 1.4 72.0 - - - +
95A SER* 1.4 59.1 + - - +
97A ALA* 3.2 6.7 + - - +
98A VAL* 2.9 42.4 + - + +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR 3.2 17.3 + - - -
94A MET* 1.4 75.1 - - - +
96A LEU* 1.4 57.0 + - - +
98A VAL* 3.3 7.9 + - - +
99A ALA* 3.0 28.9 + - - +
145A HIS* 2.9 17.5 + - - -
176A ILE* 3.5 19.1 - - - +
180A TRP* 2.9 33.3 + - - -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE 3.2 15.6 + - - +
93A LEU* 3.5 11.4 - - + +
94A MET 3.3 0.2 - - - -
95A SER* 1.4 77.2 - - - +
97A ALA* 1.4 56.0 + - - +
99A ALA* 3.4 4.5 + - - +
100A ASP* 3.0 52.4 + - - +
142A SER* 3.7 36.1 - - - +
145A HIS* 3.7 19.0 + - + -
146A LEU* 3.7 15.3 - - + -
149A ILE* 4.0 12.3 - - + -
376A ASN* 3.5 20.4 - - - +
377A PRO* 3.8 17.5 - - + -
380A TYR* 6.3 0.9 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASN* 3.4 29.2 - - - +
75A VAL* 3.9 17.9 - - + -
76A ILE* 3.7 19.5 - - + -
93A LEU 2.9 18.3 + - - +
94A MET* 3.5 5.8 - - - +
96A LEU* 1.4 71.9 - - - +
98A VAL* 1.4 59.6 + - - +
101A LEU* 2.9 30.0 + - - +
377A PRO* 4.2 3.1 - - + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.8 22.9 - - + -
94A MET* 2.9 29.8 + - + +
95A SER* 3.3 11.4 + - - +
97A ALA* 1.4 72.4 - - - +
99A ALA* 1.4 59.2 + - - +
101A LEU* 3.2 5.8 + - + +
102A LEU* 2.9 47.3 + - + +
180A TRP* 5.3 5.4 - - + -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER 3.0 12.8 + - - +
96A LEU* 3.5 11.2 - - - +
98A VAL* 1.4 73.4 - - - +
100A ASP* 1.3 65.2 + - - +
102A LEU* 3.3 7.0 + - - +
103A VAL* 3.2 26.2 + - - +
138A PHE* 3.8 13.8 - - + +
141A ALA* 4.3 14.1 - - + -
142A SER* 5.0 3.6 - - - +
145A HIS* 5.1 1.1 - - + -
180A TRP* 3.7 29.4 - - + -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 3.4 11.4 - - - +
72A ASN* 3.4 25.4 - - - +
96A LEU* 3.0 28.5 + - - +
99A ALA* 1.3 72.3 - - - +
101A LEU* 1.3 64.0 + - - +
103A VAL* 3.4 10.8 + - - +
104A GLY 3.3 15.2 + - - -
142A SER* 3.3 24.2 - - - -
373A SER* 3.0 35.4 - - - +
374A GLY* 4.8 0.7 - - - -
376A ASN* 4.3 0.5 - - - +
377A PRO* 3.3 16.3 - - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 5.0 2.0 - - - -
69A ILE* 3.8 31.0 - - + +
72A ASN* 3.9 11.2 - - + +
73A THR* 3.7 28.9 - - + -
76A ILE* 3.8 20.6 - - + -
97A ALA 2.9 19.8 + - - +
98A VAL* 3.2 8.5 + - + +
100A ASP* 1.3 75.3 - - - +
102A LEU* 1.4 58.0 + - + +
104A GLY* 3.3 3.1 + - - -
105A LEU* 3.1 44.7 + - + +
2007A OLB 5.0 3.1 - - + -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A VAL* 2.9 37.5 + - + +
99A ALA* 3.3 8.0 + - - +
101A LEU* 1.4 74.0 - - + +
103A VAL* 1.4 59.3 + - - +
105A LEU* 4.8 3.4 - - + -
106A PHE* 2.9 63.4 + - + +
107A VAL 3.8 0.5 + - - -
138A PHE* 3.6 42.3 - - + -
180A TRP* 5.1 2.2 - - + -
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA 3.2 15.9 + - - +
100A ASP* 3.6 15.9 - - - +
101A LEU 3.3 0.2 - - - -
102A LEU* 1.4 76.2 - - - +
104A GLY* 1.3 55.2 + - - +
107A VAL* 2.9 31.5 + - + -
108A MET* 2.8 54.9 + - + -
135A ASP 5.8 0.2 - - - +
138A PHE* 3.3 29.6 - - + +
139A SER* 4.6 7.9 - - - +
370A TYR* 4.2 13.2 - - + -
373A SER* 5.8 6.7 - - - -
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Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.6 15.8 - - - +
68A THR* 3.8 21.5 - - - +
69A ILE* 3.6 13.4 - - - +
100A ASP 3.3 4.9 + - - -
101A LEU 3.3 7.4 + - - -
103A VAL* 1.3 79.8 - - - +
105A LEU* 1.3 54.9 + - - +
108A MET* 4.1 10.5 - - - +
109A PRO* 3.3 20.1 - - - +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 3.9 27.1 - - + -
101A LEU* 3.1 44.0 + - + +
102A LEU* 4.9 2.9 - - + -
104A GLY* 1.3 78.3 - - - +
106A PHE* 1.3 84.6 + - + +
109A PRO* 3.3 17.2 - - - +
110A ILE* 5.9 0.3 - - - +
2003A CLR 5.8 1.6 - - + -
2007A OLB 5.2 9.9 - - + -
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 2.9 45.2 + - + +
105A LEU* 1.3 97.8 - - + +
107A VAL* 1.3 63.6 + - + +
109A PRO* 4.1 2.7 - - - -
110A ILE* 3.3 21.8 - - - +
131A TRP* 3.8 6.4 - - - -
134A LEU* 4.6 22.3 - - + +
138A PHE* 5.2 2.5 - + + -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU 4.6 0.4 - - - +
103A VAL* 2.9 25.2 + - + +
106A PHE* 1.3 82.2 - - - +
108A MET* 1.3 64.7 - - - +
109A PRO 3.5 0.4 - - - -
110A ILE 3.4 2.3 + - - -
111A ALA* 3.1 11.4 + - - +
131A TRP* 3.0 24.1 + - + +
134A LEU* 3.8 17.5 - - + +
135A ASP* 3.3 57.0 - - + +
138A PHE* 4.2 11.4 - - + -
139A SER* 5.7 0.2 - - - +
370A TYR* 3.4 14.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il