Contacts of the strand formed by residues 89 - 101 (chain A) in PDB entry 4LDD
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 MET 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ASN* 3.4 7.3 - - - +
81A VAL* 2.9 40.8 + - + +
88A LEU* 1.3 90.9 + - + +
90A LYS* 1.3 63.8 + - - +
92A ILE* 3.5 25.1 - - + -
168A LEU 5.5 8.7 - - - +
169A PRO* 5.9 4.5 - - + -
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ASN* 4.1 13.0 - - - +
89A MET* 1.3 78.7 - - - +
91A GLN* 1.3 88.7 + - + +
92A ILE* 3.6 6.5 - - - +
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Residues in contact with GLN 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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78A MET* 3.4 30.8 - - + +
79A VAL 3.3 3.5 + - - -
80A ASN* 2.8 31.0 + - - +
90A LYS* 1.3 90.0 - - + +
92A ILE* 1.3 59.8 + - - +
93A PRO* 3.7 4.3 - - - +
177A THR* 2.8 30.4 + - - +
178A ALA* 5.9 1.2 - - - +
187C PRO 4.9 2.6 - - - +
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Residues in contact with ILE 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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77A ALA 3.1 3.8 - - - +
78A MET* 3.5 2.2 - - - -
79A VAL* 2.8 50.3 + - + +
81A VAL* 4.2 13.7 - - + +
89A MET* 3.5 53.8 - - + +
90A LYS 3.6 5.2 - - - +
91A GLN* 1.3 73.7 - - - +
93A PRO* 1.3 78.1 - - + +
163A LEU* 4.3 11.9 - - + -
164A PRO* 4.1 21.3 - - + -
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Residues in contact with PRO 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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76A GLU* 4.6 9.4 - - + +
77A ALA 3.4 5.6 - - - +
78A MET* 3.4 20.4 - - + -
91A GLN 3.7 5.8 - - - +
92A ILE* 1.3 98.2 - - + +
94A ILE* 1.3 60.4 + - - +
95A TRP 4.0 1.1 + - - -
162A VAL 4.0 6.6 - - - +
163A LEU* 4.2 1.4 - - - +
164A PRO* 4.4 10.5 - - + +
70C SER* 5.7 4.5 - - - -
100C VAL* 5.9 0.9 - - - +
186C LEU* 4.0 31.7 - - + +
187C PRO 3.5 23.3 - - - +
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Residues in contact with ILE 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 LEU 3.1 17.5 - - - +
76A GLU* 3.6 2.3 - - - -
77A ALA* 2.7 36.4 + - + +
79A VAL* 3.6 30.7 - - + -
92A ILE 3.9 5.8 - - - +
93A PRO* 1.3 75.0 - - - +
95A TRP* 1.3 59.2 + - - +
96A LEU* 3.2 30.1 + - + +
122A ILE* 4.7 9.2 - - + -
133A VAL* 4.9 4.0 - - + -
162A VAL* 3.7 23.3 - - + +
163A LEU* 3.6 15.5 - - + -
174A PHE* 3.6 22.0 - - + -
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Residues in contact with TRP 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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74A ILE* 3.5 42.4 - - + -
75A LEU 4.0 1.6 - - - -
76A GLU* 5.0 4.9 - - + +
93A PRO 4.0 1.6 - - - -
94A ILE* 1.3 69.0 - - - +
96A LEU* 1.3 59.2 + - - +
97A PRO* 3.2 29.3 - - + +
161A PHE 5.5 1.3 - - - -
162A VAL* 3.2 30.5 + - - +
182A ILE* 4.0 19.1 - - + -
72C ALA* 3.9 12.5 - - + +
74C ILE* 3.6 26.3 - - + +
95C TRP* 5.2 0.2 - + - -
97C PRO* 4.8 6.8 - - + +
99C GLY* 5.1 8.6 + - - -
100C VAL* 3.5 29.4 - - + -
184C GLN* 3.9 34.5 - - + -
186C LEU* 3.8 27.4 - - + +
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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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74A ILE* 4.1 2.2 - - - +
75A LEU* 2.7 52.3 + - + +
77A ALA* 4.8 6.3 - - + -
94A ILE* 3.6 34.8 - - + +
95A TRP* 1.3 72.1 - - - +
97A PRO* 1.3 59.7 - - - +
98A LEU* 3.2 12.6 + - + +
122A ILE* 3.8 29.2 - - + -
133A VAL* 5.0 7.0 - - + -
135A VAL* 4.1 16.2 - - + -
157A PHE* 3.5 31.2 - - + -
162A VAL* 3.7 12.8 - - + -
179A LEU* 6.0 1.1 - - + -
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Residues in contact with PRO 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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73A PHE 4.8 0.4 - - - +
74A ILE* 3.8 22.2 - - + -
95A TRP* 3.2 27.8 - - + +
96A LEU* 1.3 81.3 - - - +
98A LEU* 1.3 67.0 + - - +
99A GLY* 3.3 2.5 - - - +
155A GLN* 3.4 12.3 + - - -
157A PHE* 3.5 17.4 - - + -
161A PHE* 5.0 10.3 - - + -
162A VAL* 4.8 4.9 - - + -
95C TRP* 5.0 3.8 - - + +
97C PRO* 4.3 28.0 - - + -
161C PHE* 3.6 10.4 - - + -
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Residues in contact with LEU 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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73A PHE* 2.7 33.8 + - + +
75A LEU* 3.7 35.0 - - + -
96A LEU* 3.2 17.4 + - + +
97A PRO* 1.3 71.5 - - - +
99A GLY* 1.3 57.0 + - - +
115A ILE* 4.3 20.2 - - + -
135A VAL* 5.1 5.4 - - + -
147A LEU* 3.9 20.1 - - + +
148A ARG 4.9 1.4 + - - -
149A LEU* 3.6 33.2 - - + -
150A LEU* 6.1 2.0 - - + -
155A GLN* 3.1 29.5 + - - +
157A PHE* 5.3 0.9 - - + -
181A LEU* 4.8 0.7 - - + -
161C PHE* 3.3 6.4 - - - -
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Residues in contact with GLY 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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72A ALA* 3.4 4.9 - - - +
73A PHE* 2.9 31.9 + - - +
97A PRO* 3.3 4.0 - - - +
98A LEU* 1.3 81.4 - - - +
100A VAL* 1.3 66.0 + - - -
101A ALA 4.3 0.2 + - - -
147A LEU* 3.5 6.6 - - - +
95C TRP* 5.1 7.2 + - - +
161C PHE* 4.1 19.5 - - - -
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Residues in contact with VAL 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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70A SER* 4.9 6.5 - - - -
71A SER 3.7 5.2 - - - +
72A ALA* 4.5 0.7 - - + +
99A GLY* 1.3 77.4 - - - +
101A ALA* 1.3 67.7 + - - +
146A PRO* 3.8 13.9 - - - +
147A LEU* 3.5 11.5 - - - +
186A LEU* 3.8 24.9 - - + -
93C PRO 6.0 0.7 - - - +
95C TRP* 3.7 29.6 - - + -
160C GLU 4.7 5.2 - - - +
161C PHE* 3.4 23.9 + - - +
162C VAL* 3.8 16.6 - - - +
163C LEU 4.7 5.2 - - - +
164C PRO* 4.9 14.6 - - + -
165C PRO* 5.0 3.8 - - - +
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Residues in contact with ALA 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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70A SER* 3.6 2.8 - - - -
71A SER* 2.9 38.8 + - - +
73A PHE* 3.7 25.2 - - + -
100A VAL* 1.3 78.4 - - - +
102A ASP* 1.3 65.2 - - - +
103A GLN* 5.3 0.7 - - - +
111A THR* 4.7 4.5 - - + +
145A HIS* 4.5 9.2 - - + -
146A PRO* 4.2 12.1 - - + -
147A LEU* 4.2 12.3 - - + -
165C PRO* 5.6 0.2 - - - -
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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