Contacts of the strand formed by residues 29 - 38 (chain B) in PDB entry 1DFV
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B GLN* 1.3 77.8 - - - +
30B LYS* 1.3 63.0 + - - -
31B TRP* 4.1 3.8 - - - -
54B THR 3.6 1.4 - - - +
55B ILE* 3.2 9.5 - - - -
56B TYR* 2.8 39.4 + - - -
140B ARG* 3.2 6.5 - - - -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLY* 1.3 72.7 - - - -
31B TRP* 1.3 64.6 + - - +
32B TYR* 3.7 32.6 + - + -
53B ALA* 4.3 13.0 - - + -
54B THR 3.7 2.7 - - - -
55B ILE* 4.1 27.3 - - + +
139B GLY 4.4 2.3 - - - +
140B ARG* 3.1 28.7 + - - +
176B ILE 3.5 21.2 + - - +
177B ASP* 3.6 20.3 + - - -
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Residues in contact with TRP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 2.9 40.4 + + - -
29B GLY 4.1 2.7 - - - -
30B LYS* 1.3 73.2 - - - +
32B TYR* 1.3 63.2 + - - +
33B VAL 3.9 0.7 + - - -
53B ALA* 3.4 2.4 - - - +
54B THR* 2.7 44.3 + - - +
56B TYR* 3.7 28.0 - + - -
113B THR* 3.8 12.1 - - - -
115B TYR* 4.1 8.3 - - - -
117B GLN 3.8 2.9 - - - -
118B HIS* 3.6 45.1 - - - -
119B ALA* 3.8 4.0 - - + -
138B TYR* 3.4 37.0 - + + -
139B GLY 3.5 17.0 - - - -
140B ARG* 3.2 46.8 - - - +
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 3.7 25.2 + - + +
31B TRP* 1.3 74.5 - - - +
33B VAL* 1.3 60.4 + - - +
34B VAL* 3.2 6.9 + - + +
51B MET* 4.0 18.4 - - + -
52B TYR 4.1 1.3 - - - -
53B ALA* 3.9 11.9 - - + -
138B TYR* 3.3 4.2 - - - -
139B GLY 2.7 36.4 + - - +
140B ARG 3.7 18.6 - - - -
141B THR* 3.3 29.6 - - - +
142B LYS* 3.6 25.9 + - + -
176B ILE* 3.2 35.3 + - + -
177B ASP* 2.9 20.4 + - - -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TRP 4.9 1.1 - - - +
32B TYR* 1.3 71.3 - - - +
34B VAL* 1.3 58.4 + - - +
35B GLY 3.5 22.9 - - - +
36B LEU* 4.1 19.5 - - + -
51B MET* 3.4 17.3 - - - +
52B TYR* 3.3 56.8 + - + +
54B THR* 4.3 3.6 - - - +
136B THR* 4.2 8.5 - - + -
137B LEU 3.6 3.8 - - - -
138B TYR* 3.6 24.5 - - + -
169B PRO* 3.7 12.3 - - + +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR 3.6 13.9 - - - +
33B VAL* 1.3 73.7 - - - +
35B GLY* 1.3 58.8 + - - +
51B MET* 3.8 23.3 - - + -
137B LEU* 2.9 20.0 + - + +
139B GLY 4.3 1.3 - - - +
141B THR 3.9 19.5 - - - +
142B LYS 4.2 7.6 - - - +
143B GLU* 4.3 1.1 - - - +
144B LEU* 3.4 21.1 - - + -
149B LYS* 3.2 34.1 - - - +
168B PHE* 3.3 20.8 - - - +
169B PRO* 3.5 13.3 - - - +
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Residues in contact with GLY 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 3.4 7.5 - - - +
34B VAL* 1.3 81.8 - - - +
36B LEU* 1.3 60.9 + - - -
136B THR* 3.2 5.0 - - - -
137B LEU* 2.7 43.0 + - - -
152B PHE* 3.7 12.1 - - - -
167B VAL 3.7 6.5 - - - -
168B PHE* 4.1 4.0 - - - -
169B PRO* 4.1 0.9 - - - -
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 4.1 15.7 - - + -
35B GLY* 1.3 73.0 - - - -
37B ALA* 1.3 60.3 + - - +
41B ILE* 3.6 33.7 - - + -
49B GLN* 3.9 34.5 - - + +
52B TYR* 4.3 14.4 - - + +
134B LYS* 4.3 9.0 - - + +
135B ILE 3.6 3.1 - - - +
136B THR* 3.7 25.4 - - + -
152B PHE* 3.6 2.3 - - - -
167B VAL* 2.7 53.6 + - + +
169B PRO* 4.2 7.4 - - + +
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 1.3 76.8 - - - +
38B GLY* 1.3 56.2 - - - +
41B ILE* 3.2 6.0 - - - +
134B LYS* 3.0 6.2 - - - +
135B ILE* 2.6 37.9 + - + +
152B PHE* 3.7 9.2 - - + -
156B SER* 3.5 27.1 - - - +
161B LEU* 3.8 11.2 - - + -
165B HIS 3.1 13.7 - - - +
166B ILE* 4.1 7.0 - - + -
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 1.3 74.8 - - - +
39B ASN* 1.3 59.4 + - - -
40B ALA 3.0 5.6 - - - -
41B ILE* 3.0 25.8 + - - +
133B PHE 3.3 15.5 - - - -
134B LYS* 3.8 1.1 - - - -
161B LEU* 3.2 20.5 - - - +
165B HIS* 3.1 17.2 + - - +
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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