Contacts of the helix formed by residues 84 - 103 (chain A) in PDB entry 1LAP
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 GLU 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LYS* 6.0 3.8 - - - -
74A ALA* 4.2 15.0 - - + +
75A GLY 2.7 18.7 + - - +
77A ASP* 4.5 17.1 - - + +
82A TRP* 3.4 23.9 + - + +
83A HIS* 1.3 70.5 - - - +
85A GLY* 1.3 59.3 + - - +
87A GLU* 3.2 5.6 + - + +
88A ASN* 2.8 50.4 + - - +
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.7 25.1 + - - +
83A HIS* 3.3 11.5 - - - -
84A GLU* 1.3 80.1 - - - +
86A LYS* 1.3 62.0 + - - +
88A ASN* 3.2 8.1 + - - +
89A ILE* 3.0 29.6 + - - +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS* 3.4 35.8 - - + +
84A GLU 3.3 0.2 - - - -
85A GLY* 1.3 76.4 - - - +
87A GLU* 1.3 57.7 + - - +
89A ILE* 3.1 6.8 + - + +
90A ARG* 2.9 52.8 + - - +
115A ASP* 3.0 38.0 + - - +
117A GLN* 5.5 5.7 - - - +
118A ALA* 4.0 11.5 - - + +
392A GLU* 3.4 51.1 + - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 3.6 48.9 - - + -
83A HIS 3.4 9.9 + - - +
84A GLU* 3.2 11.6 + - - +
86A LYS* 1.3 78.5 - - - +
88A ASN* 1.3 64.8 + - - +
90A ARG* 2.9 21.0 + - - +
91A ALA* 3.0 25.4 + - - +
393A THR 3.8 3.3 - - - +
394A GLY* 3.8 7.6 - - - -
460A VAL* 5.7 1.9 - - - +
461A PRO* 5.5 4.5 - - - +
462A TYR* 2.6 41.6 + - - -
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Residues in contact with ASN 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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48A ALA* 4.7 14.9 - - + +
49A GLY 5.4 0.9 + - - -
68A GLY 4.9 0.9 - - - +
69A LEU* 3.3 29.3 - - - +
70A GLY* 4.2 6.9 - - - -
71A LYS 4.6 1.6 + - - +
74A ALA* 4.3 10.4 - - - +
84A GLU* 2.8 42.0 + - - +
85A GLY* 3.3 10.1 - - - +
87A GLU* 1.3 78.3 - - - +
89A ILE* 1.4 55.8 + - + +
91A ALA* 3.4 6.4 + - - +
92A ALA* 2.9 33.6 + - - +
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Residues in contact with ILE 89 (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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9A TYR* 6.4 0.7 - - + -
69A LEU* 4.4 16.4 - - + -
85A GLY 3.0 18.5 + - - +
86A LYS* 3.1 9.4 + - + +
88A ASN* 1.4 71.5 - - + +
90A ARG* 1.3 65.6 + - - +
93A VAL* 3.0 26.3 + - + +
113A CYS* 3.4 38.4 - - + +
114A GLY 4.8 0.9 - - - -
115A ASP* 3.7 23.1 - - + +
118A ALA* 3.9 3.8 - - + -
119A ALA* 3.6 36.1 - - + +
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Residues in contact with ARG 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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83A HIS 5.0 0.6 + - - -
86A LYS* 2.9 33.2 + - - +
87A GLU* 2.9 40.9 + - - +
89A ILE* 1.3 69.9 - - - +
91A ALA* 1.3 66.1 + - - +
94A ALA* 3.0 22.3 + - - +
118A ALA* 3.4 22.7 - - + +
121A GLU* 3.0 28.7 + - + -
122A GLY* 3.5 21.2 - - - +
125A LEU* 5.2 0.4 - - - -
392A GLU 3.1 24.0 + - - -
393A THR* 3.4 19.1 + - - +
394A GLY* 4.5 0.2 - - - -
462A TYR* 3.6 40.6 - - + -
473A ARG* 3.6 4.1 - - - +
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Residues in contact with ALA 91 (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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49A GLY* 4.9 11.2 - - - -
87A GLU 3.0 18.4 + - - +
88A ASN* 3.5 6.7 - - - +
90A ARG* 1.3 78.2 - - - +
92A ALA* 1.3 62.2 + - - +
94A ALA* 3.5 2.8 + - - +
95A ALA* 3.2 20.8 + - - +
98A ARG* 5.6 0.7 + - - -
461A PRO* 3.8 29.6 - - + +
462A TYR* 3.8 12.5 - - + +
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Residues in contact with ALA 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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49A GLY* 4.3 11.4 - - - +
67A VAL* 3.7 20.0 - - + +
68A GLY 3.4 24.5 - - - +
69A LEU* 3.6 20.0 - - + -
88A ASN 2.9 19.6 + - - +
89A ILE 4.2 0.4 - - - +
91A ALA* 1.3 69.4 - - - +
93A VAL* 1.3 62.1 - - - +
95A ALA* 3.3 5.4 + - - +
96A GLY 3.0 22.3 + - - -
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Residues in contact with VAL 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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5A VAL* 4.3 11.8 - - + +
67A VAL* 4.9 2.2 - - + -
89A ILE* 3.0 19.5 + - + +
90A ARG 4.1 1.3 - - - +
92A ALA* 1.3 77.1 - - + +
94A ALA* 1.4 55.9 + - - +
96A GLY* 3.0 2.3 + - - -
97A CYS* 2.9 31.3 + - - +
110A VAL* 3.7 22.0 - - + -
113A CYS* 4.0 27.6 - - - -
119A ALA* 3.3 36.8 - - + +
122A GLY* 4.6 0.4 - - - -
123A ALA* 3.6 16.6 - - + +
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Residues in contact with ALA 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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90A ARG 3.0 16.2 + - - +
91A ALA 3.8 2.7 - - - +
93A VAL* 1.4 74.1 - - - +
95A ALA* 1.4 56.1 + - - +
97A CYS* 3.4 4.5 + - - +
98A ARG* 2.9 41.5 + - - +
122A GLY 3.3 24.3 + - - +
126A GLY* 3.6 16.6 - - - -
462A TYR* 3.7 20.2 - - + -
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Residues in contact with ALA 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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49A GLY 3.8 15.7 - - - +
51A THR* 3.6 19.7 - - + +
91A ALA 3.2 11.2 + - - +
92A ALA 3.6 5.8 - - - +
93A VAL 3.3 0.2 - - - -
94A ALA* 1.4 78.9 - - - +
96A GLY* 1.3 60.9 + - - +
98A ARG* 4.0 14.9 - - - +
99A GLN* 3.4 26.5 + - - +
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Residues in contact with GLY 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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5A VAL* 3.7 14.9 - - - +
51A THR* 3.8 3.3 - - - +
65A VAL* 4.0 6.1 - - - +
67A VAL* 3.8 22.9 - - - -
92A ALA 3.0 10.5 + - - -
93A VAL 3.0 3.1 + - - -
95A ALA* 1.3 73.9 - - - +
97A CYS* 1.3 63.9 + - - +
99A GLN* 3.0 15.1 + - - +
100A ILE* 3.1 14.2 + - - +
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Residues in contact with CYS 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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5A VAL* 4.3 8.3 - - - -
93A VAL* 2.9 20.3 + - - +
94A ALA* 3.7 7.2 - - - +
96A GLY* 1.3 75.5 - - - +
98A ARG* 1.3 58.0 + - - +
100A ILE* 3.1 9.0 + - - +
101A GLN 3.0 22.2 + - - -
108A VAL* 4.3 11.7 - - + -
110A VAL* 3.8 21.1 - - - -
123A ALA* 3.8 27.8 - - - -
127A LEU* 3.5 29.6 - - + +
141A VAL* 5.1 0.5 - - - +
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Residues in contact with ARG 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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91A ALA 5.6 0.6 + - - -
94A ALA* 2.9 28.1 + - - +
95A ALA* 4.0 11.0 - - - +
97A CYS* 1.3 75.7 - - - +
99A GLN* 1.3 65.2 + - + +
101A GLN* 3.8 7.0 - - - +
102A ASP* 3.0 33.0 + - - +
126A GLY* 2.9 49.6 + - - +
127A LEU* 4.5 1.3 - - + +
461A PRO 2.7 26.8 + - - -
462A TYR* 3.6 13.9 + - - +
463A LEU 4.2 3.4 + - - +
464A ARG* 3.9 39.4 - - - +
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Residues in contact with GLN 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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51A THR* 3.8 22.3 + - - +
53A THR* 4.2 11.8 + - + +
65A VAL* 4.0 19.7 - - + -
95A ALA 3.4 14.6 + - - +
96A GLY 3.0 8.7 + - - +
98A ARG* 1.3 76.0 - - - +
100A ILE* 1.3 64.5 + - - +
102A ASP* 3.3 15.1 + - - +
103A LEU* 3.2 28.4 + - + +
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Residues in contact with ILE 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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3A GLY* 4.0 10.3 - - - -
4A LEU 4.7 0.2 - - - +
5A VAL* 4.3 2.5 - - + -
63A SER* 3.8 26.7 - - - +
65A VAL* 3.5 29.2 - - + -
96A GLY 3.1 6.3 + - - +
97A CYS 3.1 9.5 + - - +
99A GLN* 1.3 78.1 - - - +
101A GLN* 1.3 60.0 + - - +
103A LEU* 3.3 9.6 + - + +
105A ILE* 3.3 50.3 + - + +
107A SER 4.2 0.9 - - - +
108A VAL* 3.8 39.9 - - + -
141A VAL* 4.8 2.7 - - + -
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Residues in contact with GLN 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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97A CYS 3.0 7.9 + - - +
98A ARG* 3.9 5.4 + - - +
99A GLN 3.3 0.4 - - - -
100A ILE* 1.3 74.6 - - - +
102A ASP* 1.3 60.1 + - - +
104A GLU* 2.8 24.0 + - - +
105A ILE 4.6 0.9 - - - +
127A LEU* 3.8 32.0 - - + +
129A GLU* 5.7 0.7 - - - +
138A LYS* 4.0 19.4 - - + +
139A VAL* 2.9 31.2 - - + +
140A VAL* 4.6 2.9 - - - -
141A VAL* 3.6 19.7 + - + +
464A ARG* 2.7 43.9 + - - +
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Residues in contact with ASP 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 ARG* 3.0 26.6 + - - +
99A GLN* 3.3 16.3 + - - +
101A GLN* 1.3 75.9 + - - +
103A LEU* 1.3 58.3 + - + +
104A GLU* 3.3 9.5 + - - +
138A LYS* 6.0 1.9 - - - +
464A ARG* 4.5 13.5 + - - -
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Residues in contact with LEU 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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53A THR* 4.4 7.2 - - + -
55A TYR* 4.0 27.4 - - + +
63A SER* 3.3 31.4 - - - +
99A GLN* 3.2 18.1 + - + +
100A ILE* 3.8 8.7 - - + +
101A GLN 3.1 1.4 - - - -
102A ASP* 1.3 75.8 - - + +
104A GLU* 1.3 67.2 + - - +
105A ILE* 3.2 17.8 + - + +
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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