Contacts of the strand formed by residues 97 - 114 (chain B) 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 ALA 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.6 15.3 - - + -
90B LEU* 4.8 3.8 - - + +
91B THR 3.1 14.8 - - - +
92B THR* 3.9 12.8 - - - +
95B LYS 3.5 5.3 + - - +
96B GLN* 1.3 76.5 + - - +
98B ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 98 (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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90B LEU* 3.6 12.3 - - - +
91B THR* 3.0 30.2 + - - +
96B GLN* 5.4 5.6 - - - +
97B ALA* 1.3 76.1 - - - +
99B TRP* 1.3 67.7 + - + +
100B ARG* 3.1 20.0 + - + +
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Residues in contact with TRP 99 (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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42B VAL* 4.0 23.1 - - + -
49B PHE* 4.8 3.8 - + - -
51B GLN* 4.4 13.5 - - - -
88B LYS* 4.0 33.0 - - + -
89B ALA* 3.5 9.9 - - - -
90B LEU* 4.0 29.0 - - + +
98B ALA* 1.3 77.2 - - + +
100B ARG* 1.3 61.7 + - - +
44Y ILE* 3.3 46.7 - - + +
45Y ASN* 5.8 3.2 - - - +
47Y SER* 6.1 0.4 - - - -
49Y PHE* 3.6 34.1 - + + -
99Y TRP* 3.7 34.3 - + - -
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 3.7 23.0 + - - +
34B LYS* 6.1 1.0 - - - +
36B VAL* 3.7 19.4 - - - +
88B LYS* 4.2 3.8 - - - -
89B ALA* 2.8 39.9 + - - +
91B THR* 3.1 23.9 + - - +
93B ASP* 4.1 17.4 + - - +
96B GLN* 3.8 22.3 + - - +
98B ALA* 3.1 42.2 + - - +
99B TRP* 1.3 76.3 - - - +
101B PHE* 1.3 61.8 + - - +
102B ILE* 3.4 9.6 + - + +
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Residues in contact with PHE 101 (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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222A GLU* 4.0 48.0 - - + -
30B ASP* 3.6 6.7 + - - +
31B ILE* 3.2 41.0 + - + +
86B PHE* 4.1 16.8 - - + -
87B VAL 3.3 10.8 - - - -
88B LYS* 3.7 54.5 - - + -
100B ARG* 1.3 70.6 - - - +
102B ILE* 1.3 62.2 + - - +
21Y TRP* 3.6 29.4 - + - -
52Y TYR* 4.2 20.6 - - + -
53Y PHE* 5.9 0.2 - - - -
54Y PHE 5.9 0.2 - - - -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 4.4 3.4 - - + -
28B ALA* 4.0 21.8 - - + -
29B THR 3.8 4.7 - - - +
30B ASP* 4.8 2.2 - - - -
36B VAL* 4.0 27.8 - - + -
38B VAL* 4.7 5.2 - - + -
53B PHE* 3.9 27.6 - - + -
85B THR 3.4 2.3 - - - +
86B PHE* 3.4 4.1 - - - -
87B VAL 2.9 38.7 + - - +
89B ALA* 4.0 8.5 - - + -
91B THR* 4.3 8.3 - - + -
100B ARG* 4.0 10.3 - - + +
101B PHE* 1.3 77.1 - - - +
103B ARG* 1.3 63.0 + - - +
104B ILE* 3.4 28.1 + - + +
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Residues in contact with ARG 103 (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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147A ILE* 5.2 7.5 + - + +
219A PRO* 6.6 0.2 - - - -
28B ALA* 5.3 2.8 - - - +
29B THR* 3.1 41.5 + - - +
30B ASP 5.7 1.8 - - - -
84B HIS* 3.7 55.8 + - + +
85B THR 3.5 3.8 - - - +
86B PHE* 4.2 23.0 - - + -
102B ILE* 1.3 72.1 - - - +
104B ILE* 1.3 64.8 + - - +
105B ASP* 4.4 1.0 + - - +
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Residues in contact with ILE 104 (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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25B LYS* 4.0 24.2 - - + -
28B ALA* 5.8 0.2 - - + -
53B PHE* 4.3 13.5 - - + -
54B PHE 3.8 11.9 - - - +
55B GLU* 3.6 16.6 - - + +
84B HIS* 3.2 3.6 - - - -
85B THR* 2.7 54.0 + - + +
87B VAL* 4.0 21.3 - - + -
102B ILE* 3.8 32.8 - - + +
103B ARG* 1.3 79.8 - - - +
105B ASP* 1.3 76.5 + - - +
106B THR* 3.5 0.7 + - - -
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Residues in contact with ASP 105 (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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55B GLU* 3.4 22.4 + - - +
56B THR 3.2 31.2 + - - +
57B LYS* 3.4 25.5 + - + +
82B THR* 3.9 13.9 - - + +
83B THR 3.8 5.4 - - - -
84B HIS* 3.0 24.8 + - - -
103B ARG 5.2 0.7 - - - +
104B ILE* 1.3 80.0 - - - +
106B THR* 1.3 59.4 + - - +
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Residues in contact with THR 106 (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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54B PHE 4.8 3.4 - - - +
56B THR* 3.1 27.1 + - - +
83B THR* 2.8 12.8 + - - +
84B HIS 3.2 27.7 + - - -
85B THR* 3.2 26.7 + - + -
105B ASP* 1.3 75.3 - - - +
107B ALA* 1.3 61.2 + - - +
83Y THR* 4.7 9.5 - - - +
84Y HIS 5.4 1.2 - - - +
85Y THR* 3.8 21.4 - - - +
106Y THR* 3.6 28.3 + - + +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.4 13.1 + - - +
82B THR* 3.2 11.6 - - - +
83B THR* 2.9 35.5 + - - -
106B THR* 1.3 80.2 - - - +
108B CYS* 1.3 64.3 + - - +
109B VAL* 4.0 3.1 - - + -
83Y THR* 5.0 4.3 - - + -
107Y ALA* 3.3 33.9 - - + -
109Y VAL* 4.7 5.8 - - + -
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Residues in contact with CYS 108 (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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14B VAL* 6.0 0.3 - - - +
15B CYS* 3.6 32.0 - - + +
16B ASP 3.9 10.8 - - - +
17B SER* 4.2 13.3 - - - -
58B CYS* 2.0 55.2 - - + +
60B ALA 5.0 0.2 - - - -
80B CYS* 3.8 9.9 - - - -
81B THR 3.4 2.7 - - - -
107B ALA* 1.3 75.1 - - - +
109B VAL* 1.3 61.3 + - - +
109Y VAL* 4.0 13.8 - - - +
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Residues in contact with VAL 109 (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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14B VAL* 6.1 0.4 - - - -
15B CYS* 4.1 3.6 - - - -
80B CYS* 3.4 3.6 - - - -
81B THR* 2.9 44.9 + - + +
83B THR* 3.2 27.4 - - + +
107B ALA* 4.7 7.2 - - + -
108B CYS* 1.3 77.6 - - - +
110B CYS* 1.3 62.9 + - - +
111B VAL* 5.0 4.0 - - + -
13Y SER* 5.2 10.5 - - - +
107Y ALA* 4.9 3.6 - - + -
108Y CYS 4.0 21.5 - - - +
109Y VAL* 4.6 10.3 - - + +
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Residues in contact with CYS 110 (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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14B VAL* 3.6 21.0 - - + +
15B CYS* 3.9 1.5 - - - -
68B CYS* 2.0 49.4 - - - -
71B ILE* 4.1 3.6 - - - -
78B SER* 4.1 5.2 - - - -
79B TYR 3.7 0.7 - - - -
109B VAL* 1.3 78.0 - - - +
111B VAL* 1.3 68.8 + - - +
112B LEU* 4.1 2.0 - - - -
13Y SER* 4.0 3.1 + - - -
14Y VAL* 3.2 49.4 + - + +
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Residues in contact with VAL 111 (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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78B SER* 3.4 19.9 - - - -
79B TYR* 3.0 34.1 + - + +
81B THR* 4.0 26.5 - - + -
109B VAL* 4.8 4.0 - - + +
110B CYS* 1.3 77.9 - - - +
112B LEU* 1.3 74.7 + - - +
11Y GLU* 3.2 37.5 - - + +
12Y PHE 3.6 12.6 - - - +
13Y SER* 5.6 3.4 - - - +
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Residues in contact with LEU 112 (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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71B ILE* 4.1 13.2 - - + -
76B TRP* 4.0 18.6 - - + -
77B ASN 3.6 3.6 - - - +
78B SER* 4.0 16.8 - - - -
79B TYR* 6.3 0.4 - - - -
110B CYS* 4.1 2.7 - - - -
111B VAL* 1.3 86.2 - - - +
113B SER* 1.3 61.9 + - - +
10Y GLY 3.7 1.2 - - - +
11Y GLU* 2.9 10.3 - - - +
12Y PHE* 2.8 70.4 + - + +
14Y VAL* 3.8 21.3 - - + -
69Y ARG* 3.6 23.8 - - + +
70Y GLY* 3.8 13.9 - - - -
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Residues in contact with SER 113 (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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76B TRP* 3.3 15.6 - - - -
77B ASN* 3.1 43.8 + - - +
79B TYR* 5.8 1.9 - - - -
112B LEU* 1.3 76.0 - - - +
114B ARG* 1.3 63.1 + - - +
95G LEU* 3.5 32.7 + - - -
97G TYR* 3.6 14.6 + - - -
10Y GLY 3.8 7.4 - - - -
11Y GLU* 4.1 3.5 - - - +
12Y PHE* 5.5 0.9 - - - -
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Residues in contact with ARG 114 (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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75A GLU 4.1 21.7 + - - +
75B HIS* 4.0 19.6 + - - +
76B TRP* 3.7 38.4 - - + -
77B ASN* 4.4 6.1 - - - +
113B SER* 1.3 77.6 - - - +
115B LYS* 1.3 69.7 + - - +
116B ALA 3.5 2.4 + - - -
97G TYR* 5.7 1.9 - - - -
99G TYR* 5.2 0.2 + - - -
147G THR 4.7 2.8 + - - -
149G PHE* 3.7 22.4 - - - -
174G GLU* 4.9 6.9 - - - +
218G THR* 3.5 38.3 + - - +
10Y GLY 4.6 3.6 + - - +
12Y PHE* 6.0 0.6 - - + -
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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