Contacts of the strand formed by residues 96 - 114 (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 GLN 96 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Y THR 3.9 0.5 - - - +
92Y THR* 3.3 9.7 - - - +
93Y ASP* 3.2 26.0 + - + +
95Y LYS* 1.3 97.0 - - + +
97Y ALA* 1.3 63.4 + - - +
98Y ALA* 4.0 13.6 + - - +
100Y ARG* 4.4 15.6 + - - +
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Residues in contact with ALA 97 (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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39Y LEU* 5.3 7.2 - - + -
90Y LEU* 4.9 10.3 - - + +
91Y THR 3.4 7.4 - - - +
92Y THR* 4.3 9.6 - - - +
96Y GLN* 1.3 77.2 - - - +
98Y ALA* 1.3 62.2 + - - +
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Residues in contact with ALA 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90Y LEU* 4.3 3.4 - - - -
91Y THR* 2.9 39.8 + - - +
96Y GLN* 4.0 13.4 - - - +
97Y ALA* 1.3 76.1 - - - +
99Y TRP* 1.3 66.4 + - - +
100Y ARG* 3.3 25.1 + - + +
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Residues in contact with TRP 99 (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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43B ASN* 4.9 8.7 - - - +
49B PHE* 3.6 36.2 - + + -
99B TRP* 3.7 36.1 - + - -
222X GLU* 5.2 2.8 - - - +
42Y VAL* 3.4 32.0 - - + +
44Y ILE* 4.5 14.4 - - + +
49Y PHE* 4.8 4.5 - + - -
51Y GLN* 4.4 11.9 - - - -
88Y LYS* 3.6 53.2 + - + +
89Y ALA 3.4 16.2 - - - -
90Y LEU* 3.9 18.4 - - + +
98Y ALA* 1.3 72.2 - - - +
100Y ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 100 (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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222X GLU* 5.2 6.5 - - - +
30Y ASP* 4.4 21.3 + - + +
32Y LYS* 6.0 1.8 - - - +
36Y VAL* 4.3 12.1 - - - -
88Y LYS* 4.3 2.5 - - - -
89Y ALA 3.0 27.9 + - - +
91Y THR* 3.1 20.6 + - - +
92Y THR 4.8 0.6 - - - -
93Y ASP* 2.9 46.9 + - - +
96Y GLN* 4.4 18.8 + - - +
98Y ALA* 3.5 24.7 - - + +
99Y TRP* 1.3 77.0 - - - +
101Y PHE* 1.3 65.1 + - - +
102Y ILE* 3.3 7.7 + - + +
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Residues in contact with PHE 101 (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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21B TRP* 3.6 25.4 - + - -
52B TYR* 4.0 22.2 - + + -
54B PHE 5.8 0.2 - - - -
222X GLU* 3.8 47.3 + - + -
30Y ASP* 3.2 5.7 - - - +
31Y ILE* 2.9 47.2 + - + +
86Y PHE* 4.1 20.9 - - + -
87Y VAL 3.5 5.4 - - - -
88Y LYS* 3.6 58.8 - - + -
100Y ARG* 1.3 71.5 - - - +
102Y ILE* 1.3 60.1 + - - +
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Residues in contact with ILE 102 (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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25Y LYS* 4.5 1.3 - - - -
28Y ALA* 3.7 32.3 - - + -
30Y ASP* 4.0 8.1 - - + +
36Y VAL* 4.0 9.2 - - + -
38Y VAL* 4.3 8.5 - - + -
53Y PHE* 3.9 17.0 - - + -
86Y PHE* 3.6 6.5 - - - -
87Y VAL 2.9 37.4 + - - +
89Y ALA* 3.7 22.2 - - + -
91Y THR* 4.0 17.5 - - + -
100Y ARG* 3.8 9.2 - - + +
101Y PHE* 1.3 78.4 - - - +
103Y ARG* 1.3 61.4 + - - +
104Y ILE* 3.4 21.6 + - + +
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Residues in contact with ARG 103 (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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145X THR* 5.6 8.1 - - - +
25Y LYS* 4.9 5.5 + - - -
28Y ALA* 5.1 3.5 - - - +
29Y THR* 3.3 35.9 + - - +
30Y ASP* 4.4 1.1 - - - +
84Y HIS* 3.5 56.9 + - + -
85Y THR 3.7 4.0 - - - +
86Y PHE* 4.4 21.7 - - + -
101Y PHE 4.3 0.2 + - - -
102Y ILE* 1.3 72.2 - - - +
104Y ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 104 (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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25Y LYS* 3.7 34.1 - - - +
53Y PHE* 4.2 19.1 - - + -
54Y PHE 4.0 10.1 - - - +
55Y GLU* 3.6 20.4 - - + -
84Y HIS* 3.2 4.6 - - - -
85Y THR* 2.9 46.9 + - + +
87Y VAL* 4.1 19.5 - - + -
102Y ILE* 3.7 25.6 - - + +
103Y ARG* 1.3 78.1 - - - +
105Y ASP* 1.3 70.1 + - - +
106Y THR* 3.6 0.9 + - + -
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Residues in contact with ASP 105 (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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55Y GLU* 3.3 32.3 + - - +
56Y THR 3.0 28.2 + - - +
57Y LYS* 3.9 15.7 + - + +
82Y THR* 4.0 13.6 - - + +
83Y THR 3.8 4.7 - - - -
84Y HIS* 3.0 28.3 + - - -
104Y ILE* 1.3 75.2 - - - +
106Y THR* 1.3 59.8 + - - +
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Residues in contact with THR 106 (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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83B THR* 5.0 7.8 - - - +
84B HIS 5.7 0.9 - - - +
85B THR* 3.7 20.1 - - - +
106B THR* 3.6 28.2 + - + +
54Y PHE* 4.5 5.8 - - + +
56Y THR* 3.3 23.8 + - - +
83Y THR* 2.7 13.0 + - - +
84Y HIS 3.2 28.2 + - - -
85Y THR* 3.2 26.5 + - + -
104Y ILE* 5.0 0.9 - - + -
105Y ASP* 1.3 76.0 - - - +
107Y ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 107 (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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83B THR* 5.2 4.7 - - + -
107B ALA* 3.3 33.4 - - + -
109B VAL* 4.9 4.7 - - + -
56Y THR* 3.4 12.2 + - - -
82Y THR* 3.3 9.4 - - - +
83Y THR* 2.8 37.7 + - + -
106Y THR* 1.3 81.8 - - - +
108Y CYS* 1.3 62.1 + - - +
109Y VAL* 3.9 4.7 - - + -
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Residues in contact with CYS 108 (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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109B VAL* 4.0 14.5 - - - +
15Y CYS* 3.8 29.2 - - + +
16Y ASP 3.7 14.1 - - - +
17Y SER* 4.1 15.2 - - - -
57Y LYS 4.4 0.2 - - - +
58Y CYS* 2.0 56.5 - - - +
60Y ALA 4.8 0.7 - - - -
80Y CYS* 3.8 8.3 - - - -
81Y THR 3.4 2.0 - - - -
107Y ALA* 1.3 75.5 - - - +
109Y VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 109 (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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13B SER* 5.3 8.3 - - - +
107B ALA* 4.7 5.2 - - + -
108B CYS 4.0 21.1 - - - +
109B VAL* 4.6 7.2 - - + +
15Y CYS* 4.2 2.5 - - - -
80Y CYS* 3.5 1.4 - - - -
81Y THR* 2.8 47.8 + - + +
83Y THR* 3.2 29.8 - - + +
107Y ALA* 4.5 8.5 - - + -
108Y CYS* 1.3 78.1 - - - +
110Y CYS* 1.3 62.8 + - - +
111Y VAL* 4.9 4.7 - - + -
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Residues in contact with CYS 110 (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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13B SER* 4.2 4.7 + - - -
14B VAL* 3.5 45.5 + - + +
14Y VAL* 3.6 21.5 - - + +
15Y CYS* 3.6 2.2 - - - -
68Y CYS* 2.0 49.1 - - - -
71Y ILE* 4.4 2.0 - - - -
78Y SER* 4.2 5.4 - - - -
79Y TYR 3.5 3.8 - - - -
109Y VAL* 1.3 76.4 - - - +
111Y VAL* 1.3 69.4 + - - +
112Y LEU* 4.3 2.5 - - - -
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Residues in contact with VAL 111 (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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11B GLU* 3.1 33.4 - - + +
12B PHE 4.0 13.5 - - - +
13B SER* 5.1 5.4 - - - +
78Y SER* 3.3 9.0 - - - -
79Y TYR* 2.9 51.4 + - + +
81Y THR* 3.9 26.9 - - + -
109Y VAL* 4.6 4.3 - - + +
110Y CYS* 1.3 77.8 - - - +
112Y LEU* 1.3 68.5 + - - +
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Residues in contact with LEU 112 (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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10B GLY 3.8 0.3 - - - +
11B GLU* 3.3 7.2 - - - +
12B PHE* 3.0 54.3 + - + +
14B VAL* 4.0 12.8 - - + -
69B ARG* 3.4 27.6 - - + +
70B GLY* 3.8 13.5 - - - +
71Y ILE* 3.8 22.0 - - + -
76Y TRP* 3.8 26.5 - - + -
77Y ASN 3.4 2.9 - - - +
78Y SER* 3.8 20.2 - - - -
79Y TYR* 6.0 0.2 - - - -
110Y CYS* 4.3 1.5 + - - -
111Y VAL* 1.3 83.7 - - - +
113Y SER* 1.3 61.0 + - - +
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Residues in contact with SER 113 (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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10B GLY 3.5 7.9 - - - -
11B GLU* 4.3 5.1 - - - +
12B PHE* 4.9 1.6 - - - -
76Y TRP* 3.4 14.6 - - - -
77Y ASN* 2.9 47.8 + - - +
79Y TYR* 5.4 3.3 - - - -
112Y LEU* 1.3 75.4 - - - +
114Y ARG* 1.3 63.6 + - - +
95Z LEU* 3.7 32.0 - - - -
97Z TYR* 3.6 13.9 + - - -
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Residues in contact with ARG 114 (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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10B GLY 4.2 5.1 + - - +
12B PHE* 5.4 2.0 - - + -
75Y HIS* 4.1 20.0 + - - +
76Y TRP* 4.1 35.1 - - + -
77Y ASN* 4.6 4.9 - - - +
113Y SER* 1.3 77.1 - - - +
115Y LYS* 1.3 73.6 + - - +
116Y ALA* 3.6 2.1 + - - +
95Z LEU* 5.5 0.2 - - - -
97Z TYR* 6.0 0.7 - - - -
99Z TYR* 5.4 0.2 + - - -
147Z THR 5.0 2.4 + - - -
149Z PHE* 3.3 37.0 - - - -
174Z GLU* 4.8 8.3 - - - +
218Z THR* 3.5 32.1 - - - +
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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