Contacts of the strand formed by residues 98 - 114 (chain D) in PDB entry 2GOO
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 VAL 98 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 4.9 2.7 - - + -
90D LEU* 3.7 34.3 - - + -
91D TYR 3.3 6.7 - - - +
92D LEU* 3.6 19.5 - - + -
96D GLU 4.1 1.1 + - - +
97D LYS* 1.3 71.3 - - - +
99D VAL* 1.3 58.1 + - - +
17F ASN* 4.3 10.9 + - - +
44F THR* 4.3 8.5 - - + +
46F LYS* 5.7 4.3 - - - -
55F VAL* 3.8 29.4 - - + +
56F LYS* 2.6 27.0 + - + +
81F VAL* 3.9 26.5 - - + -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D MET 3.8 0.5 - - - +
90D LEU* 3.4 8.2 - - - +
91D TYR* 2.7 70.3 + - + +
93D ASP* 4.0 24.7 - - + +
97D LYS* 3.9 10.5 - - + +
98D VAL* 1.3 75.7 - - - +
100D LEU* 1.3 72.6 + - - +
101D LYS* 4.8 7.0 - - + -
17F ASN* 6.3 0.2 - - - +
56F LYS* 3.6 2.9 - - - +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D SER* 4.9 3.8 - - - -
89D MET 3.6 9.4 - - - +
90D LEU* 3.8 14.1 - - + -
99D VAL* 1.3 78.9 - - - +
101D LYS* 1.3 72.8 + - - +
102D ASN* 5.0 5.4 - - - +
13F PHE* 6.4 1.8 - - + -
29F GLU* 6.1 1.1 - - - +
42F PHE* 3.8 26.2 - - + -
56F LYS* 3.5 22.5 - - + +
58F GLY* 6.0 1.1 - - - -
59F CYS 4.9 4.7 - - - +
60F TRP* 3.7 31.2 - - + -
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Residues in contact with LYS 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D SER* 3.5 1.9 - - - -
89D MET* 2.8 37.7 + - - +
91D TYR* 3.8 23.0 + - + +
99D VAL* 4.1 6.0 + - + -
100D LEU* 1.3 80.4 - - - +
102D ASN* 1.3 68.4 + - - +
103D TYR* 3.6 48.1 + - + +
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Residues in contact with ASN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ILE 3.4 2.7 - - - -
88D SER* 2.7 34.1 + - - +
100D LEU* 5.0 8.0 - - - +
101D LYS* 1.3 77.1 + - - +
103D TYR* 1.3 63.0 + - - +
104D GLN* 3.6 18.9 + - - +
59F CYS 5.5 2.4 + - - -
61F LEU* 3.5 27.9 - - + +
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Residues in contact with TYR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TRP* 5.3 5.2 - + - -
86D ALA* 3.1 6.1 - - - -
87D ILE* 2.8 33.5 + - + +
89D MET* 3.8 47.8 - - + +
91D TYR* 3.1 28.9 + + - -
101D LYS* 3.6 42.5 + - + +
102D ASN* 1.3 70.4 - - - +
104D GLN* 1.3 62.8 + - - +
106D MET* 3.4 31.0 - - + +
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ALA* 3.8 21.3 - - - +
102D ASN* 3.6 21.4 + - - +
103D TYR* 1.3 75.8 - - - +
105D ASP* 1.3 83.1 + - - +
106D MET* 3.4 5.9 + - - +
61F LEU* 5.5 0.4 - - - +
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Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 3.6 51.2 + - + +
85D SER* 3.5 10.5 + - - +
86D ALA 4.4 0.2 - - - +
104D GLN* 1.3 82.9 + - - +
106D MET* 1.3 61.2 + - - +
107D VAL 3.6 1.1 - - - -
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Residues in contact with MET 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 5.7 0.4 - - + -
38D TYR* 3.1 59.9 + - + +
40D ALA* 3.9 7.3 - - - +
84D LEU* 5.0 1.6 - - - -
85D SER 2.7 9.8 + - - +
87D ILE* 4.0 24.0 - - + +
89D MET* 4.1 15.7 - - - -
103D TYR* 3.4 40.6 - - + +
104D GLN 3.7 5.4 - - - +
105D ASP* 1.3 77.1 - - - +
107D VAL* 1.3 61.9 + - + +
108D VAL* 4.3 0.3 + - - +
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D TYR* 3.8 5.2 - - + -
39D HIS 3.4 26.0 - - - +
40D ALA 3.7 2.7 - - - -
41D PHE* 3.9 11.7 - - + -
84D LEU* 2.9 10.0 - - - -
85D SER* 2.8 46.4 + - - +
86D ALA 5.0 0.2 - - - +
87D ILE* 3.7 28.7 - - + -
106D MET* 1.3 84.3 - - - +
108D VAL* 1.3 73.5 + - - +
109D GLU* 4.0 6.7 - - - +
37F LYS* 5.2 3.6 - - - +
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ARG* 2.8 36.4 + - + -
40D ALA 3.0 19.5 + - - +
41D PHE* 3.6 25.1 - - + +
42D TYR* 4.4 2.5 - - - -
43D CYS* 3.7 20.6 - - - -
81D PRO* 3.6 27.4 - - + -
83D GLU 3.8 3.4 - - - -
84D LEU* 4.4 6.1 - - + -
106D MET 4.3 0.6 - - - +
107D VAL* 1.3 72.6 - - - +
109D GLU* 1.3 56.5 + - - +
110D GLY 3.6 22.0 - - - +
111D CYS* 3.8 7.2 - - - -
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ARG* 3.9 21.4 + - - +
83D GLU* 2.8 36.5 + - + +
84D LEU 4.0 2.9 - - - -
85D SER* 2.5 44.1 + - - +
107D VAL* 4.0 6.5 - - - +
108D VAL* 1.3 79.7 - - - +
110D GLY* 1.3 58.6 + - - +
37F LYS* 2.9 23.4 + - - -
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Residues in contact with GLY 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 5.4 1.3 - - - -
81D PRO* 3.3 6.4 - - - +
82D THR* 2.8 33.2 + - - -
83D GLU* 3.1 18.4 + - - +
108D VAL* 3.6 6.1 - - - +
109D GLU* 1.3 80.0 - - - +
111D CYS* 1.3 55.8 + - - -
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Residues in contact with CYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D CYS* 4.1 9.9 - - - -
15D LYS* 4.1 12.6 - - - -
16D ARG* 3.5 30.5 - - - +
43D CYS* 2.1 53.4 - - + -
54D HIS* 3.6 17.2 + - - +
55D LEU* 4.3 5.0 - - - +
56D ASN* 5.3 0.2 + - - -
80D VAL 3.4 4.7 - - - -
82D THR* 3.7 5.7 + - - -
108D VAL* 3.8 5.2 - - - -
110D GLY* 1.3 73.4 - - - -
112D GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D CYS* 4.0 4.2 - - - -
55D LEU* 3.0 20.0 - - - -
78D CYS 3.3 1.0 - - - +
79D CYS* 3.4 3.1 - - - -
80D VAL* 2.8 34.2 + - - +
82D THR* 3.6 13.5 - - - +
111D CYS* 1.3 77.1 - - - +
113D CYS* 1.3 66.0 + - - -
114D ARG 3.9 0.2 + - - -
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Residues in contact with CYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D CYS* 3.8 17.7 - - - -
47D CYS* 2.1 53.6 - - + -
51D LEU* 4.1 9.9 - - + -
55D LEU* 3.0 24.9 + - + -
57D SER* 3.3 36.5 + - - +
61D ALA* 3.7 5.4 - - - +
77D ALA* 4.4 3.1 - - + -
78D CYS 3.3 2.0 - - - -
112D GLY* 1.3 73.8 - - - -
114D ARG* 1.3 63.4 + - - +
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Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ASN* 3.1 33.1 + - - +
58D THR* 3.8 30.1 + - - +
60D HIS* 4.7 7.1 + - - -
61D ALA* 3.7 21.1 + - - +
64D GLN* 5.2 3.6 - - - +
77D ALA* 3.7 4.6 - - - +
78D CYS* 2.9 38.8 + - - +
80D VAL* 3.7 27.4 - - + -
81D PRO 5.5 0.6 + - - -
82D THR* 3.4 36.4 + - + +
113D CYS* 1.3 78.6 + - - +
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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