Contacts of the strand formed by residues 85 - 94 (chain A) in PDB entry 2ZLE
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 LYS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LYS* 5.3 21.4 - - - +
78A VAL 3.5 4.9 - - - +
79A GLN* 3.9 32.1 - - + +
83A GLY 3.6 4.9 + - - +
84A ARG* 1.3 75.4 - - - +
86A PHE* 1.3 76.1 + - - +
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Residues in contact with PHE 86 (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 LYS* 3.8 6.2 - - - +
78A VAL* 2.8 35.5 + - + +
80A LEU* 3.2 33.4 - - + -
84A ARG* 3.6 44.0 - - + -
85A LYS* 1.3 81.9 - - - +
87A ASP* 1.3 68.0 + - - +
104A ILE* 3.4 27.6 - - + -
105A GLN 3.9 4.9 - - - +
106A ASN* 3.4 26.9 - - + -
107A PRO* 4.1 2.0 - - + -
108A LYS* 4.1 13.2 - - + -
110A LEU* 4.6 2.7 - - + -
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Residues in contact with ASP 87 (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* 5.6 1.2 - - - +
76A ILE 4.0 3.1 - - - +
77A LYS* 3.8 25.3 - - - +
78A VAL 5.1 0.4 - - - -
86A PHE* 1.3 82.0 - - - +
88A ALA* 1.3 58.8 + - - +
104A ILE* 3.4 5.2 - - - +
105A GLN* 2.5 51.3 + - + +
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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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76A ILE* 2.9 53.7 + - + +
78A VAL* 3.9 8.3 - - + -
87A ASP* 1.3 77.3 - - - +
89A LYS* 1.3 68.9 + - - +
102A ILE* 3.8 15.5 - - + -
103A GLN 3.2 15.0 - - - +
104A ILE* 4.3 1.1 - - - -
105A GLN* 4.2 0.7 - - - +
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Residues in contact with LYS 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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76A ILE* 4.9 2.9 - - - -
88A ALA* 1.3 77.6 - - - +
90A MET* 1.3 69.2 + - - +
102A ILE* 3.4 6.1 - - - -
103A GLN* 3.0 31.3 + - + +
105A GLN* 3.2 44.5 - - + +
318A ASP* 5.6 8.3 - - + +
321A SER* 3.6 33.8 + - - +
322A ILE 5.3 0.4 + - - -
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Residues in contact with MET 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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70A VAL* 3.5 39.3 - - + +
73A ALA* 5.5 4.9 - - + +
76A ILE* 5.0 10.4 - - + +
89A LYS* 1.3 76.7 - - - +
91A VAL* 1.3 61.3 + - - +
92A GLY* 3.0 50.0 - - - +
93A LYS* 3.9 17.5 - - + +
101A LEU 4.2 5.4 - - - +
102A ILE* 4.4 4.3 - - - -
314A GLN 6.0 1.3 - - - +
318A ASP* 3.5 38.6 - - + +
372A ARG* 4.1 0.9 + - - -
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Residues in contact with VAL 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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62A TYR* 4.6 11.0 - - + +
90A MET* 1.3 76.9 - - - +
92A GLY* 1.3 58.9 + - - +
101A LEU* 3.1 47.2 + - + +
102A ILE* 3.4 18.2 - - - +
103A GLN* 4.0 11.0 - - + +
209A MET 4.1 15.4 - - - +
210A VAL* 4.6 6.1 - - - +
213A GLY 3.9 6.4 - - - +
315A ASN* 4.7 0.6 - - - +
318A ASP* 5.1 1.1 - - - -
372A ARG* 3.2 38.1 + - - +
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Residues in contact with GLY 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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90A MET* 3.0 17.8 - - - +
91A VAL* 1.3 82.1 - - - +
93A LYS* 1.3 60.1 + - - +
100A ALA* 3.5 1.2 - - - +
101A LEU 2.8 24.8 + - - +
209A MET* 3.3 24.2 - - - -
213A GLY 4.7 6.3 - - - -
214A GLN* 6.0 0.2 - - - -
315A ASN* 5.5 2.0 - - - -
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Residues in contact with LYS 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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67A ASN* 3.1 21.0 - - - +
70A VAL* 5.1 0.4 - - + -
71A ASP* 2.5 50.6 + - - +
72A ASN 4.3 1.4 - - - +
90A MET* 4.0 18.8 - - + -
92A GLY* 1.3 76.0 - - - +
94A ASP* 1.3 62.7 - - - +
95A PRO* 4.1 11.1 - - + +
99A ILE 3.6 3.8 - - - -
100A ALA* 3.9 10.1 - - + +
209A MET* 3.3 12.7 - - - +
214A GLN* 5.7 3.6 - - - +
215A VAL* 4.9 1.6 + - - +
312A SER 5.2 4.7 - - - -
313A SER* 3.4 18.0 - - - -
314A GLN 4.5 17.8 + - - +
316A GLN* 4.8 17.2 - - - +
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Residues in contact with ASP 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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67A ASN* 4.6 1.7 - - - +
93A LYS* 1.3 77.8 - - - +
95A PRO* 1.3 63.5 - - - +
96A ARG* 4.0 3.8 + - - +
97A SER* 2.9 27.3 + - - +
98A ASP 3.0 21.9 + - - -
99A ILE 3.0 11.6 + - - +
205A LEU* 3.3 5.6 - - + +
209A MET* 3.5 15.5 - - + -
215A VAL* 3.6 20.7 - - + +
217A ARG* 3.3 42.0 + - - -
310A GLN* 5.4 0.5 - - - +
312A SER* 5.9 0.7 - - - -
313A SER* 4.0 5.1 - - - -
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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