Contacts of the strand formed by residues 25 - 40 (chain A) in PDB entry 3KVH
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 SER 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLY 3.9 2.8 + - - -
24A TRP* 1.3 75.9 - - - +
26A HIS* 1.3 63.4 + - - +
66A PHE* 4.0 23.8 - - - -
107A ARG 3.1 13.2 + - - -
108A VAL* 3.4 7.7 - - - -
109A VAL* 3.0 26.9 + - - +
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Residues in contact with HIS 26 (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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17A ALA 3.2 31.0 + - - -
18A MET* 4.6 1.8 - - + -
20A LEU* 4.8 3.2 + - + +
21A GLY 5.5 0.2 + - - -
24A TRP* 3.7 21.4 + - - +
25A SER* 1.3 79.3 - - - +
27A SER* 1.3 59.1 + - - +
66A PHE* 3.4 8.3 - - - -
67A VAL* 2.9 36.7 + - + +
69A ARG* 3.4 40.6 + - + -
74A LEU* 4.1 15.4 - - + +
109A VAL* 3.5 16.8 - - + +
111A HIS* 3.0 27.1 + - - +
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Residues in contact with SER 27 (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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26A HIS* 1.3 74.7 - - - +
28A CYS* 1.3 56.1 + - - +
29A HIS* 2.9 32.1 + - - -
65A GLY* 3.1 18.8 + - - -
66A PHE* 3.6 22.8 + - - +
108A VAL* 4.5 5.2 - - - -
109A VAL 3.0 10.5 + - - -
110A ALA* 4.7 5.2 - - - -
111A HIS* 2.8 36.2 + - - -
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Residues in contact with CYS 28 (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 SER* 1.3 79.4 - - - +
29A HIS* 1.3 62.3 + - - +
64A GLY* 3.3 4.0 - - - -
65A GLY 2.9 29.5 + - - +
67A VAL* 3.8 18.6 - - + -
74A LEU* 3.6 32.1 - - - -
78A LEU* 3.8 27.1 - - + +
81A VAL* 4.2 0.9 - - - +
111A HIS* 3.4 27.1 - - - -
113A TYR* 4.3 6.1 - - + -
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Residues in contact with HIS 29 (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 SER* 2.9 33.8 + - - -
28A CYS* 1.3 75.0 + - - +
30A ALA* 1.3 61.1 + - - +
55A ARG* 4.8 11.7 + - - -
62A PHE* 3.1 40.4 + - + -
63A PRO 3.2 5.2 - - - +
64A GLY* 3.5 16.8 + - - -
65A GLY* 3.5 10.5 + - - -
78A LEU* 4.0 5.4 - - - -
110A ALA* 5.4 3.4 - - + +
111A HIS 2.9 12.6 + - - +
112A LEU* 3.7 4.9 - - + +
113A TYR* 2.9 29.5 + - - +
166A VAL* 5.8 6.0 - - + +
172A GLN* 4.7 18.9 + - - +
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Residues in contact with ALA 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 HIS* 1.3 74.5 - - - +
31A MET* 1.3 59.5 + - - +
32A LEU* 3.8 16.7 + - + -
62A PHE* 3.6 6.8 - - - +
63A PRO* 2.9 34.0 + - + +
78A LEU* 4.3 0.6 - - + +
82A LEU* 3.7 17.0 - - + -
91A LEU* 3.6 31.6 - - + -
112A LEU* 4.9 0.2 - - - -
113A TYR* 3.3 6.1 - - + +
114A ALA* 5.8 0.4 - - - -
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Residues in contact with MET 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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30A ALA* 1.3 69.0 - - - +
32A LEU* 1.3 61.2 + - - +
33A TYR* 3.7 7.8 - - + -
50A VAL* 3.6 30.1 - - + -
62A PHE* 3.7 30.5 - - + -
112A LEU* 4.5 6.6 - - + +
113A TYR 2.8 15.8 + - - +
114A ALA* 3.2 7.5 - - + +
115A ARG 3.0 24.3 + - - +
173A LEU* 4.4 4.9 - - + -
176A ALA* 3.4 31.6 - - + -
177A LEU* 4.1 8.7 - - + -
180A LEU* 4.2 6.5 - - + -
182A MET* 3.7 37.2 - - + -
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Residues in contact with LEU 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 ALA* 3.8 21.3 + - + +
31A MET* 1.3 73.2 - - - +
33A TYR* 1.3 62.4 + - - +
50A VAL* 3.6 1.7 - - - +
51A LEU* 3.0 37.6 + - + -
63A PRO* 5.5 3.8 - - + -
82A LEU* 5.4 3.1 - - + -
84A LEU* 3.7 31.0 - - + -
86A LEU* 4.9 4.3 - - + -
91A LEU* 4.5 10.1 - - + -
115A ARG* 3.5 30.1 - - + +
117A LEU* 4.2 10.3 - - + -
122A LEU* 3.8 16.0 - - + +
125A VAL* 4.2 21.1 - - + -
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Residues in contact with TYR 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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31A MET* 3.7 18.2 - - + -
32A LEU* 1.3 74.5 - - - +
34A ALA* 1.3 58.8 + - - +
48A PHE* 4.1 11.0 - + - -
49A SER 3.1 13.7 - - - +
50A VAL* 3.8 16.4 - - + -
114A ALA* 4.4 0.9 - - + -
115A ARG* 3.2 18.0 + - - -
116A GLN* 3.3 53.8 + - + +
117A LEU* 2.8 30.7 + - - +
122A LEU* 3.9 6.1 - - - +
180A LEU* 3.8 37.5 + - + +
182A MET* 3.4 28.0 - - + -
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Residues in contact with ALA 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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33A TYR* 1.3 75.9 - - - +
35A ALA* 1.3 62.0 - - - +
36A ASN* 4.3 0.2 - - - +
48A PHE* 3.3 9.1 - - - +
49A SER* 2.9 32.1 + - - -
116A GLN* 4.6 0.9 - - - -
117A LEU 3.1 20.9 - - - +
118A THR 3.6 3.6 - - - +
119A LEU* 3.6 37.0 - - + +
122A LEU* 4.1 7.4 - - + -
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Residues in contact with ALA 35 (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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34A ALA* 1.3 72.8 - - - +
36A ASN* 1.3 59.4 + - - +
37A PRO* 3.9 5.4 - - + +
47A ARG 3.5 9.4 - - - +
48A PHE* 3.7 16.7 - - + -
116A GLN* 4.1 16.4 - - - +
117A LEU 4.4 1.4 + - - -
119A LEU* 3.8 19.4 + - - +
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Residues in contact with ASN 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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34A ALA 3.5 0.8 + - - +
35A ALA* 1.3 73.4 - - - +
37A PRO* 1.3 64.2 - - - +
38A GLY* 2.9 28.4 + - - +
46A MET* 3.7 26.5 - - + +
47A ARG* 2.9 32.9 + - - +
48A PHE* 4.1 12.1 - - - -
49A SER* 2.9 29.4 + - - +
119A LEU* 3.7 20.2 - - + +
144A ARG* 4.1 9.5 - - - +
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Residues in contact with PRO 37 (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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35A ALA* 3.9 7.0 - - + +
36A ASN* 1.3 86.0 - - - +
38A GLY* 1.3 66.2 + - - +
39A GLN* 3.8 15.5 + - - +
119A LEU* 4.3 10.1 - - + -
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Residues in contact with GLY 38 (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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36A ASN* 2.9 17.7 + - - -
37A PRO* 1.3 84.4 - - - +
39A GLN* 1.3 63.7 + - - -
46A MET* 3.1 35.8 + - - +
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Residues in contact with GLN 39 (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 PRO* 3.8 12.3 + - - +
38A GLY* 1.3 80.4 + - - -
40A LEU* 1.3 61.4 + - - +
41A PHE 3.3 0.9 + - - -
42A GLY* 2.9 36.1 + - - +
43A ARG* 3.8 8.8 - - - +
44A ILE 3.2 6.8 - - - -
45A PRO* 3.3 40.5 - - - +
46A MET* 4.4 3.3 - - - +
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Residues in contact with LEU 40 (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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39A GLN* 1.3 70.1 - - - +
41A PHE* 1.3 104.7 + - + +
42A GLY 3.0 1.0 + - - -
43A ARG* 3.0 10.9 + - - +
44A ILE* 2.8 38.0 + - + +
46A MET* 3.9 29.1 - - + +
148A TYR* 3.7 36.1 - - + +
150A GLN* 5.4 3.8 - - - -
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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