Contacts of the strand formed by residues 76 - 93 (chain Y) in PDB entry 1SGF
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 TRP 76 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.2 38.4 - + - -
69B ARG* 6.2 0.9 - - + -
70B GLY* 3.6 28.3 - - - -
66Y SER 4.9 2.3 - - - +
71Y ILE* 3.7 18.5 - - + +
72Y ASP* 2.7 35.7 + - + +
73Y SER* 3.7 20.6 - - - +
75Y HIS* 1.3 90.0 - + + +
77Y ASN* 1.3 64.2 + - - +
78Y SER* 3.9 2.1 + - - -
112Y LEU* 3.8 20.9 - - + -
113Y SER 3.4 22.0 - - - +
114Y ARG* 4.1 28.3 - - + -
115Y LYS* 4.5 3.0 - - - -
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Residues in contact with ASN 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Y SER 5.6 0.4 - - - -
76Y TRP* 1.3 73.0 + - - +
78Y SER* 1.3 61.0 + - - +
79Y TYR* 5.6 0.4 - - - -
112Y LEU* 3.4 6.4 - - - +
113Y SER* 2.9 48.1 + - - +
114Y ARG 4.6 2.1 - - - +
115Y LYS* 3.4 37.4 - - + +
95Z LEU* 4.0 12.9 + - - +
97Z TYR* 3.3 34.7 - - - +
99Z TYR* 3.2 20.2 + - - -
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Residues in contact with SER 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Y ASN* 5.6 1.6 + - - +
66Y SER 3.1 23.0 + - - +
67Y GLY* 3.2 14.4 - - - -
68Y CYS* 3.1 23.0 + - - -
71Y ILE* 4.1 15.0 - - - +
76Y TRP 3.9 1.1 + - - -
77Y ASN* 1.3 76.5 - - - +
79Y TYR* 1.3 67.6 + - - +
110Y CYS* 4.2 0.4 - - - -
111Y VAL 3.3 9.9 - - - -
112Y LEU* 3.8 14.8 - - - -
97Z TYR* 5.2 0.8 + - - -
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Residues in contact with TYR 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 2.5 32.3 + - + -
2D NAG 5.6 9.0 - - + +
61Y SER* 3.9 12.8 - - - +
62Y ASN* 5.7 1.3 - - - +
67Y GLY* 4.8 0.2 - - - -
68Y CYS* 3.8 6.3 - - - -
78Y SER* 1.3 78.4 - - - +
80Y CYS* 1.3 71.5 + - - +
81Y THR* 4.0 18.6 + - + -
110Y CYS* 3.5 1.9 - - - -
111Y VAL* 2.9 49.3 + - + +
113Y SER* 5.4 3.6 - - - -
95Z PHE* 3.3 29.6 + - - -
97Z TYR* 4.7 11.7 - - - -
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Residues in contact with CYS 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Y CYS* 2.0 47.1 - - - -
58Y CYS* 4.3 2.9 - - - +
60Y ALA 3.6 15.9 - - - +
61Y SER* 3.2 23.2 + - - +
63Y PRO* 3.6 30.5 - - - -
68Y CYS* 3.8 6.5 - - - -
79Y TYR* 1.3 78.8 - - - +
81Y THR* 1.3 60.2 + - - +
108Y CYS* 3.8 10.5 - - - -
109Y VAL 3.5 4.3 - - - -
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Residues in contact with THR 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Y CYS* 3.4 6.7 - - - -
79Y TYR* 4.0 16.8 + - + -
80Y CYS* 1.3 75.2 - - - +
82Y THR* 1.3 67.4 + - - +
83Y THR* 5.1 0.4 - - - +
108Y CYS* 3.4 2.1 - - - -
109Y VAL* 2.8 53.2 + - + +
111Y VAL* 3.9 16.2 - - + -
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Residues in contact with THR 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145X THR* 5.8 0.2 - - - -
56Y THR 3.9 14.6 - - - +
57Y LYS* 4.0 9.9 - - + +
58Y CYS* 3.4 21.0 + - - +
81Y THR* 1.3 81.6 + - - +
83Y THR* 1.3 70.1 + - - +
84Y HIS* 3.4 20.4 + - - +
105Y ASP* 4.0 21.8 - - + +
107Y ALA 3.3 11.4 - - - +
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Residues in contact with THR 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 6.0 2.5 - - + +
106B THR 4.7 11.2 - - - +
107B ALA* 5.0 3.1 - - + -
145X THR* 4.4 17.8 - - - +
81Y THR* 3.7 1.1 + - - +
82Y THR* 1.3 74.9 - - - +
84Y HIS* 1.3 69.4 + - - +
105Y ASP* 3.7 2.6 - - - -
106Y THR* 2.7 32.5 + - - +
107Y ALA* 2.8 28.9 + - + +
109Y VAL* 3.2 29.6 - - + +
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Residues in contact with HIS 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 4.6 4.2 - - - -
56B THR* 5.6 0.9 + - - -
106B THR 5.4 1.2 - - - +
145X THR* 2.9 37.6 + - - +
82Y THR* 3.4 24.5 + - - +
83Y THR* 1.3 80.4 - - - +
85Y THR* 1.3 59.6 + - - +
86Y PHE* 6.1 2.0 - - + -
103Y ARG* 3.5 62.6 + - + -
104Y ILE 3.2 12.1 - - - +
105Y ASP* 3.0 31.2 + - - -
106Y THR* 3.2 8.2 + - - -
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Residues in contact with THR 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 3.4 29.2 + - - +
56B THR* 5.6 0.6 + - - -
85B THR* 5.5 2.2 - - + -
106B THR* 3.8 19.7 - - + +
84Y HIS* 1.3 72.8 - - - +
86Y PHE* 1.3 71.9 + - - +
87Y VAL* 4.1 20.4 - - + -
102Y ILE 3.6 0.7 - - - +
103Y ARG* 3.7 3.8 - - - -
104Y ILE* 2.9 36.8 + - + +
106Y THR* 3.3 32.8 - - + +
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Residues in contact with PHE 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.8 22.4 - + + -
54B PHE* 3.7 55.5 + + + +
87B VAL* 6.0 0.3 - - - +
145X THR* 5.4 4.9 - - + -
218X GLU 5.0 1.6 - - - -
219X PRO* 3.9 28.9 - - + -
220X CYS* 4.8 2.9 - - - -
30Y ASP 5.3 0.2 - - - -
31Y ILE* 3.8 42.8 - - + -
84Y HIS* 6.0 1.6 - - + -
85Y THR* 1.3 83.3 + - - +
87Y VAL* 1.3 63.1 + - - +
101Y PHE* 4.1 14.8 - - + -
102Y ILE 3.6 13.5 - - - +
103Y ARG* 4.4 21.3 - - + -
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Residues in contact with VAL 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR* 6.3 0.2 - - + -
86B PHE 5.8 0.7 - - - +
87B VAL* 4.3 37.5 - - + -
88B LYS 5.7 0.9 - - - +
53Y PHE* 4.4 20.2 - - + -
85Y THR* 4.1 17.7 - - + -
86Y PHE* 1.3 78.2 - - - +
88Y LYS* 1.3 75.2 + - - +
89Y ALA 3.5 1.0 + - - -
101Y PHE* 3.7 3.4 - - - -
102Y ILE* 2.9 32.1 + - - +
104Y ILE* 4.1 20.9 - - + -
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Residues in contact with LYS 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 3.9 39.6 - - + +
50B ARG 4.4 9.2 + - - +
51B GLN* 6.1 0.2 - - - +
52B TYR* 5.7 4.2 - - - +
87B VAL* 5.8 0.6 - - - +
222X GLU* 5.3 4.2 + - - -
51Y GLN* 4.9 0.5 - - - +
53Y PHE* 5.2 0.7 - - - -
87Y VAL* 1.3 80.9 - - - +
89Y ALA* 1.3 61.0 + - - +
99Y TRP* 3.6 54.9 + - + +
100Y ARG 3.8 3.4 - - - -
101Y PHE* 3.6 47.3 - - + -
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Residues in contact with ALA 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y VAL* 4.4 3.1 - - + -
51Y GLN* 3.8 8.7 - - - +
53Y PHE* 3.5 36.6 - - + -
87Y VAL 3.5 0.4 + - - -
88Y LYS* 1.3 74.4 - - - +
90Y LEU* 1.3 63.7 + - - +
91Y THR* 3.4 2.5 + - - -
99Y TRP* 3.4 9.2 - - - -
100Y ARG 3.0 32.6 + - - +
102Y ILE* 3.7 20.2 - - + -
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Residues in contact with LEU 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y VAL* 3.6 0.9 - - - +
39Y LEU* 3.4 42.8 + - + -
41Y GLU 3.5 24.5 - - - +
42Y VAL* 4.2 16.6 - - + -
43Y ASN* 5.0 2.7 - - + +
51Y GLN* 3.2 26.6 + - - +
89Y ALA* 1.3 73.6 - - - +
91Y THR* 1.3 68.6 + - - +
97Y ALA* 4.9 8.1 - - + +
98Y ALA* 4.0 12.1 - - - +
99Y TRP* 3.9 32.3 - - + +
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Residues in contact with THR 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y VAL* 3.7 29.2 - - + -
37Y THR 3.2 13.5 - - - +
38Y VAL* 3.9 13.7 - - + -
39Y LEU* 4.8 3.8 - - - +
89Y ALA 3.6 4.1 + - - +
90Y LEU* 1.3 83.0 - - - +
92Y THR* 1.3 61.9 + - - +
93Y ASP 4.4 0.3 + - - -
96Y GLN 3.9 0.3 - - - +
97Y ALA* 3.4 4.7 - - - +
98Y ALA 2.9 42.8 + - - +
100Y ARG* 3.1 25.8 + - - +
102Y ILE* 4.0 15.3 - - + -
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Residues in contact with THR 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y VAL* 3.1 5.3 - - - +
37Y THR* 2.8 48.0 + - + -
39Y LEU* 4.1 22.3 - - - +
91Y THR* 1.3 74.0 + - - +
93Y ASP* 1.3 62.4 + - - +
94Y GLU* 3.6 18.5 + - - +
95Y LYS 4.8 1.8 - - - +
96Y GLN 3.3 12.3 + - - +
97Y ALA* 4.3 7.3 - - - +
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Residues in contact with ASP 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y LYS* 3.4 38.4 - - - +
35Y GLU 5.2 3.3 - - - +
36Y VAL* 4.0 12.0 - - + +
92Y THR* 1.3 71.0 - - - +
94Y GLU* 1.3 67.9 + - - +
95Y LYS* 3.1 17.9 + - - +
96Y GLN* 3.2 7.9 + - + +
100Y ARG* 2.9 40.5 + - - +
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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
------------------------------------------------------------
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