Contacts of the strand formed by residues 29 - 38 (chain A) in PDB entry 4QAE
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A HIS* 1.3 78.9 + - - +
30A LYS* 1.3 62.9 + - - -
31A TRP* 3.8 4.2 + - - -
54A THR 3.7 1.9 - - - +
55A ILE* 3.4 8.7 - - - -
56A TYR* 2.8 38.7 + - - +
140A ARG* 3.6 3.4 - - - -
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Residues in contact with LYS 30 (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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29A GLY* 1.3 72.1 - - - -
31A TRP* 1.3 70.4 + - - +
32A TYR* 3.2 30.9 + - + +
53A ALA* 4.3 9.0 - - + -
54A THR 3.7 3.1 - - - -
55A ILE* 4.0 23.1 - - + +
69A VAL* 6.1 0.7 - - - -
140A ARG* 3.0 31.7 + - - +
176A ILE* 2.6 31.2 + - - +
177A ASP* 3.5 16.4 + - - +
25R THR* 4.5 18.5 + - - +
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Residues in contact with TRP 31 (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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27A PHE* 2.9 47.6 + + - -
29A GLY 3.9 2.9 - - - -
30A LYS* 1.3 75.2 - - - +
32A TYR* 1.3 62.2 + - - +
33A VAL* 5.0 0.3 - - - +
53A ALA* 3.3 4.3 - - - +
54A THR* 2.9 36.5 + - - +
56A TYR* 3.7 24.2 - + - -
113A THR* 3.8 4.5 - - - -
115A TYR* 3.6 13.0 - - - -
117A GLN 3.8 1.6 - - - -
118A HIS* 3.6 40.4 - - - -
119A ALA* 3.9 0.7 - - + -
138A TYR* 3.5 40.6 - + + -
139A GLY 3.6 16.4 - - - -
140A ARG* 3.3 49.6 - - + +
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Residues in contact with TYR 32 (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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30A LYS* 3.2 31.3 + - + +
31A TRP* 1.3 73.0 - - - +
33A VAL* 1.3 61.7 + - - +
34A VAL* 3.2 3.6 + - + -
51A MET* 3.9 13.2 - - + -
52A TRP 3.7 1.8 - - - -
53A ALA* 4.3 8.5 - - + -
138A TYR* 3.2 7.4 - - - -
139A GLY 2.8 40.0 + - - +
140A ARG 3.5 16.6 - - - -
141A THR* 3.5 29.8 - - - +
142A LYS* 3.9 20.4 - - + -
176A ILE* 3.5 44.6 - - + -
177A ASP* 3.5 12.3 + - - -
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Residues in contact with VAL 33 (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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32A TYR* 1.3 69.6 - - - +
34A VAL* 1.3 61.3 + - - +
35A GLY 3.5 24.9 - - - +
36A LEU* 4.2 5.4 - - + -
51A MET* 3.5 18.6 - - - +
52A TRP* 2.9 74.5 + - + +
53A ALA* 4.7 0.9 - - - +
54A THR* 4.3 3.8 - - - +
136A THR* 4.1 8.7 - - + -
137A LEU 3.8 2.9 - - - -
138A TYR* 4.0 19.1 - - + -
169A PRO* 3.5 14.0 - - + +
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Residues in contact with VAL 34 (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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32A TYR* 3.9 9.6 - - + +
33A VAL* 1.3 73.4 - - - +
35A GLY* 1.3 58.5 + - - +
51A MET* 4.0 7.8 - - + +
137A LEU* 2.8 16.6 + - + +
139A GLY* 4.0 7.2 - - - +
141A THR 3.7 18.4 - - - +
142A LYS* 3.5 27.4 - - - +
143A GLU* 4.4 0.7 - - - +
144A LEU* 4.0 26.5 - - + +
149A LYS* 4.1 24.2 - - - -
168A PHE* 3.4 15.1 - - - +
169A PRO* 3.4 14.4 - - - +
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Residues in contact with GLY 35 (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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33A VAL* 3.5 9.3 - - - +
34A VAL* 1.3 80.2 - - - +
36A LEU* 1.3 61.1 + - - -
136A THR* 3.4 5.0 - - - -
137A LEU* 2.8 31.4 + - - +
152A PHE* 3.7 17.5 - - - -
167A VAL 3.3 9.6 - - - -
168A PHE* 4.0 4.0 - - - -
169A PRO* 3.8 1.6 - - - -
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Residues in contact with LEU 36 (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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33A VAL* 4.2 8.3 - - + -
35A GLY* 1.3 74.7 - - - +
37A ALA* 1.3 60.7 + - - +
41A VAL* 4.1 18.2 - - + +
49A MET* 3.6 40.4 - - + -
52A TRP* 4.4 4.7 - - + -
134A TRP* 3.5 36.8 - - + -
135A VAL 3.4 11.2 - - - +
136A THR* 4.0 10.3 - - + -
152A PHE* 3.6 3.9 - - - -
165A HIS 4.0 0.5 - - - +
166A ILE 3.7 0.2 - - - -
167A VAL* 2.8 46.4 + - + +
169A PRO* 4.1 1.8 - - + +
11P CYS* 4.1 4.9 - - - -
19P CYS* 3.8 16.6 - - - -
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Residues in contact with ALA 37 (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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36A LEU* 1.3 78.8 - - - +
38A GLY* 1.3 59.2 + - - +
41A VAL* 5.2 0.4 - - - -
134A TRP* 2.9 6.0 - - - +
135A VAL* 2.7 36.8 + - + +
152A PHE* 3.7 7.6 - - + -
156A SER* 3.3 29.6 - - - +
161A LEU* 3.7 14.3 - - + +
165A HIS 3.2 13.2 - - - +
166A ILE* 4.1 7.2 - - + -
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Residues in contact with GLY 38 (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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37A ALA* 1.3 75.8 - - - +
39A ASN* 1.3 63.1 + - - -
40A GLU 3.1 4.5 + - - -
41A VAL* 3.3 15.2 - - - +
133A PHE 3.2 13.0 - - - -
134A TRP* 3.9 5.4 - - - -
161A LEU* 3.6 12.0 - - - +
165A HIS* 3.0 30.8 + - - +
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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