Contacts of the strand formed by residues 29 - 38 (chain C) in PDB entry 4ZHF
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 GLY 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C GLN* 1.3 76.9 - - - +
30C LYS* 1.3 63.1 + - - -
31C TRP* 3.7 5.7 + - - -
54C THR 3.8 0.7 - - - +
55C ILE* 3.4 8.9 - - - -
56C TYR* 2.8 35.4 + - - -
140C ARG* 3.6 3.4 - - - -
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY* 1.3 72.5 - - - -
31C TRP* 1.3 65.1 + - - +
32C TYR* 3.9 21.1 + - + +
53C ALA* 4.1 17.3 - - + -
54C THR 3.8 3.4 - - - -
55C ILE* 4.1 29.8 - - + +
69C VAL* 6.0 1.3 - - - -
140C ARG* 2.9 32.6 + - - +
175C CYS 5.3 0.4 + - - -
176C ILE 2.8 30.3 + - - +
177C ASP* 3.5 23.6 + - - +
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Residues in contact with TRP 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.0 47.5 + + - -
29C GLY 4.0 1.6 - - - -
30C LYS* 1.3 74.1 - - - +
32C TYR* 1.3 64.2 + - - +
33C VAL* 5.1 0.3 - - - +
53C ALA* 3.3 2.8 - - - +
54C THR* 2.8 39.7 + - - +
56C TYR* 3.9 24.5 - + - -
113C THR* 3.8 3.6 - - - -
115C TYR* 3.5 20.2 - - - -
117C GLN 3.6 22.9 - - - -
118C HIS* 3.6 28.0 - - - -
119C ALA* 3.9 0.7 - - + -
138C TYR* 3.3 40.4 - + + -
139C GLY 3.6 18.2 - - - -
140C ARG* 3.4 34.4 - - + +
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Residues in contact with TYR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS* 3.9 16.7 + - + +
31C TRP* 1.3 74.2 - - - +
33C VAL* 1.3 61.4 + - - +
34C VAL* 3.2 6.2 + - + -
51C MET* 4.0 14.6 - - + -
52C TYR 3.8 1.8 - - - -
53C ALA* 4.1 9.9 - - + -
138C TYR* 3.3 6.0 - - - -
139C GLY 2.7 35.6 + - - +
140C ARG* 3.4 26.9 - - - -
141C THR* 3.5 23.6 - - - +
142C LYS* 3.9 18.4 - - + -
176C ILE* 3.5 41.3 + - + -
177C ASP* 2.6 27.3 + - - +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TYR* 1.3 68.5 - - - +
34C VAL* 1.3 60.9 + - - +
35C GLY 3.6 21.8 - - - +
36C LEU* 4.0 18.8 - - + -
51C MET* 3.6 17.9 - - - +
52C TYR* 3.0 57.7 + - + +
54C THR* 4.3 6.1 - - - +
136C THR* 3.9 8.5 - - + -
137C LEU 3.8 2.9 - - - -
138C TYR* 3.9 23.6 - - + -
169C PRO* 3.7 13.6 - - + +
204C SO4 4.1 1.3 - - - +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TYR* 3.5 17.5 - - + +
33C VAL* 1.3 74.6 - - - +
35C GLY* 1.3 57.3 + - - +
51C MET* 4.1 7.6 - - + -
137C LEU* 2.8 15.7 + - + +
139C GLY* 3.8 8.5 - - - +
141C THR 3.7 22.0 - - - +
142C LYS 3.9 20.4 - - - +
144C LEU* 4.1 32.8 - - + +
149C LYS* 4.7 10.8 - - + +
168C PHE* 3.4 17.4 - - - +
169C PRO* 3.4 13.5 - - - +
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Residues in contact with GLY 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.4 10.2 - - - +
34C VAL* 1.3 80.2 - - - +
36C LEU* 1.3 61.8 + - - -
136C THR* 3.6 3.3 - - - -
137C LEU* 2.8 40.1 + - - +
152C PHE* 3.7 10.5 - - - -
167C VAL 3.5 8.1 - - - -
168C PHE* 4.0 5.6 - - - -
169C PRO* 4.1 1.1 - - - -
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 4.0 15.5 - - + -
35C GLY* 1.3 71.9 - - - +
37C ALA* 1.3 65.0 + - - +
41C ILE* 3.9 24.4 - - + +
49C GLN* 3.8 29.8 - - - +
52C TYR* 4.1 19.7 - - + +
134C LYS* 4.0 20.9 - - + +
135C ILE 3.6 2.7 - - - +
136C THR* 3.9 20.9 - - - +
152C PHE* 3.7 3.2 - - - -
166C ILE* 3.5 0.9 - - - +
167C VAL* 2.8 48.8 + - + +
169C PRO* 4.8 3.6 - - + -
202C 4OL 5.5 2.9 - - - +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 1.3 76.2 - - - +
38C GLY* 1.3 58.3 + - - +
41C ILE* 3.9 5.6 - - - -
134C LYS* 3.0 5.0 - - - +
135C ILE* 2.6 39.9 + - + +
152C PHE* 3.8 8.1 - - + -
156C SER* 3.3 26.7 - - - +
161C LEU* 3.9 8.5 - - + -
165C HIS 3.3 12.1 - - - +
166C ILE* 3.8 13.2 - - + -
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Residues in contact with GLY 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA* 1.3 75.2 - - - +
39C ASN* 1.3 58.3 + - - -
40C ALA 3.2 5.8 - - - -
41C ILE* 3.1 18.8 + - - +
133C PHE 3.2 14.1 - - - -
134C LYS* 3.9 1.3 - - - -
161C LEU* 3.5 18.8 - - - +
165C HIS* 3.0 28.0 + - - +
202C 4OL 5.5 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