Contacts of the strand formed by residues 90 - 102 (chain H) in PDB entry 4R2G
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 LYS 90 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H LYS* 5.6 0.2 - - - +
33H GLN* 5.6 4.7 - - - +
83H ILE* 3.7 21.3 - - + +
84H CYS 3.9 3.1 - - - -
85H GLU* 3.4 32.1 + - + +
88H ASP 5.8 1.1 - - - -
89H GLN* 1.3 84.7 + - - +
91H GLU* 1.3 66.4 + - - +
92H GLU* 3.7 6.0 + - + +
279K ASP* 5.6 0.8 + - - -
511K NAG 4.6 18.3 + - - +
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Residues in contact with GLU 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H LYS 3.5 24.3 + - - -
15H THR 5.8 4.0 - - - +
16H CYS* 5.9 4.9 - - + -
28H TRP* 5.5 0.5 - - - -
82H TYR 3.8 0.3 - - - +
83H ILE* 3.2 5.9 - - - -
84H CYS* 2.9 41.6 + - + +
89H GLN* 3.9 12.1 - - + +
90H LYS* 1.3 76.2 - - - +
92H GLU* 1.3 67.8 + - - +
93H VAL* 5.3 4.7 - - + +
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Residues in contact with GLU 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H LYS* 3.8 23.9 + - - +
2H LYS* 3.9 5.4 + - - +
81H THR* 3.3 23.3 - - + +
82H TYR 3.5 1.6 - - - -
83H ILE* 3.6 23.7 - - + +
90H LYS* 3.7 6.3 + - + +
91H GLU* 1.3 82.4 + - - +
93H VAL* 1.3 70.1 + - - +
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LYS* 3.5 12.6 - - + +
4H VAL* 4.0 24.5 - - + -
14H LEU* 4.3 26.0 - - + -
15H THR* 4.8 13.5 - - - +
28H TRP* 4.8 13.5 - - + -
80H ASP 3.8 0.5 - - - +
81H THR* 3.2 7.1 - - - +
82H TYR* 2.9 38.5 + - + +
91H GLU* 5.3 5.8 - - + +
92H GLU* 1.3 82.2 - - - +
94H GLN* 1.3 71.0 + - - +
95H LEU* 4.0 2.2 + - + +
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Residues in contact with GLN 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H LYS* 5.3 2.9 + - - -
2H LYS 3.4 6.1 + - - -
3H VAL* 3.2 34.8 - - + +
4H VAL 2.9 24.4 + - - -
80H ASP 3.8 6.7 - - - +
81H THR* 4.0 15.9 - - - +
93H VAL* 1.3 75.3 - - - +
95H LEU* 1.3 59.2 + - - +
96H LEU* 3.8 31.4 - - + +
164H ASN* 4.3 7.2 + - - +
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Residues in contact with LEU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 3.3 32.5 - - + +
6H GLY* 4.2 15.0 - - - +
12H VAL* 3.8 31.9 - - + -
14H LEU* 4.7 5.8 - - + -
71H ILE* 4.2 15.3 - - + -
74H LEU* 4.2 14.6 - - + -
78H ASP 4.4 11.9 - - - +
79H SER* 3.1 22.5 - - - -
80H ASP 3.1 15.9 + - - +
82H TYR* 4.3 11.2 - - + -
93H VAL* 4.0 7.3 - - + -
94H GLN* 1.3 73.4 - - - +
96H LEU* 1.3 68.3 + - - +
97H VAL* 4.2 7.6 - - + -
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Residues in contact with LEU 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H VAL* 4.6 7.2 - - + -
4H VAL 3.0 7.5 + - - -
5H LEU* 3.5 19.4 - - + +
6H GLY 2.9 26.5 + - - +
79H SER* 3.5 4.9 - - - -
80H ASP 5.5 0.2 - - - +
94H GLN* 3.8 31.2 - - + +
95H LEU* 1.3 85.0 - - - +
97H VAL* 1.3 61.5 + - - +
98H PHE* 4.1 11.0 + - + -
121H PRO* 4.0 19.7 - - + -
124H SER* 4.5 9.2 - - - -
163H GLN* 3.6 37.5 - - + +
164H ASN* 5.1 1.3 - - - +
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Residues in contact with VAL 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLY 3.2 8.7 - - - +
8H LYS* 4.0 16.6 - - + +
74H LEU* 3.9 37.2 - - + -
75H LYS 3.4 33.4 - - - +
76H ILE* 3.6 14.1 - - + +
78H ASP* 4.4 0.2 - - + -
79H SER* 2.8 25.8 + - - +
95H LEU* 4.2 10.3 - - + -
96H LEU* 1.3 77.6 - - - +
98H PHE* 1.3 63.9 + - - +
119H GLU 3.8 1.2 - - - +
121H PRO* 3.5 19.2 - - - +
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Residues in contact with PHE 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LEU* 4.2 29.4 - - + -
6H GLY 2.9 9.1 + - - +
7H LYS* 3.6 1.0 - - - -
8H LYS* 3.0 25.2 + - - -
76H ILE* 5.7 0.7 - - - -
96H LEU* 4.3 12.6 - - + -
97H VAL* 1.3 73.9 - - - +
99H GLY* 1.3 57.9 + - - +
118H LEU* 3.8 14.6 - - + -
119H GLU 3.3 5.2 - - - -
120H SER* 3.5 37.2 - - - -
121H PRO* 3.6 9.4 - - + -
124H SER* 3.9 11.0 - - - -
126H PRO* 3.7 26.0 - - + -
161H VAL* 4.0 18.4 - - + -
163H GLN* 4.1 11.7 - - + -
168H VAL* 4.8 5.4 - - + -
170H PHE* 3.1 25.1 - - + -
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Residues in contact with GLY 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LYS* 4.1 19.4 - - - +
76H ILE* 5.4 0.4 - - - +
98H PHE* 1.3 74.0 - - - +
100H LEU* 1.3 61.3 + - - -
101H THR* 4.2 2.0 - - - -
118H LEU* 3.2 9.5 - - - +
119H GLU* 2.9 41.7 + - - +
170H PHE* 3.9 6.7 - - - -
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Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H GLY* 1.3 72.7 - - - -
101H THR* 1.3 60.6 + - - +
116H LEU* 3.6 25.6 - - + -
117H THR 3.2 25.4 - - - +
118H LEU* 3.7 20.2 - - + +
128H VAL* 5.0 7.0 - - + -
130H CYS* 4.4 0.7 - - - -
144H LEU* 6.0 0.2 - - + -
159H CYS* 3.5 32.1 - - + -
161H VAL* 5.4 0.2 - - + -
170H PHE* 3.8 35.7 - - + -
172H ILE* 3.5 30.5 - - + +
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Residues in contact with THR 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H GLY 5.1 1.2 - - - -
100H LEU* 1.3 76.9 + - - +
102H ALA* 1.3 74.3 + - - +
103H ASN* 4.2 6.0 + - - +
116H LEU* 3.2 8.7 - - - +
117H THR* 2.9 41.9 + - - -
119H GLU* 4.5 13.2 + - - +
172H ILE* 4.8 1.1 - - - -
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Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H LEU 4.2 0.8 + - - -
101H THR* 1.3 83.5 - - - +
103H ASN* 1.3 64.9 + - - +
104H SER 3.7 1.1 + - - -
105H ASP* 3.8 17.2 + - - +
114H LEU* 4.4 8.7 - - + -
115H THR 4.3 3.4 - - - -
116H LEU* 4.6 3.1 - - + +
172H ILE* 4.2 13.4 - - + +
174H ILE* 3.8 29.2 - - + -
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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