Contacts of the strand formed by residues 110 - 125 (chain Y) in PDB entry 1JPY
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 SER 110 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26X LYS* 3.7 21.0 + - - +
28X ASP* 2.4 42.8 + - - -
102Y ARG* 3.8 0.3 - - - -
103Y LYS* 2.8 30.7 + - - +
104Y HIS* 3.4 22.7 - - - -
108Y SER 3.4 1.8 + - - -
109Y VAL* 1.3 73.7 - - - +
111Y PHE* 1.3 70.4 + - - +
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Residues in contact with PHE 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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10X PHE* 3.3 53.2 - + - -
11X PHE* 3.5 30.7 - + - -
25X MET* 3.9 25.8 - - + -
26X LYS 2.7 19.6 + - - +
27X LEU* 3.1 15.6 - - + +
28X ASP* 2.6 34.3 + - - -
27Y LEU* 4.6 5.8 - - + -
100Y VAL* 4.0 13.5 - - + -
101Y ARG 3.4 2.5 - - - -
102Y ARG* 3.8 13.0 - - + -
103Y LYS* 4.9 0.2 - - - -
109Y VAL* 3.7 33.0 - - + -
110Y SER* 1.3 77.2 - - - +
112Y GLN* 1.3 55.5 + - - +
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Residues in contact with GLN 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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27X LEU* 4.3 2.7 - - - -
28X ASP* 3.7 13.0 - - + +
29X ILE 3.4 13.0 + - - -
30X GLY* 3.2 31.2 + - - +
32X ILE* 3.5 29.9 - - + +
100Y VAL* 4.6 2.2 - - - -
101Y ARG* 2.7 42.0 + - + +
103Y LYS* 3.3 37.0 + - + +
111Y PHE* 1.3 75.3 - - - +
113Y LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 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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27X LEU* 4.2 21.7 - - + +
28X ASP 5.0 0.4 + - - -
30X GLY 3.9 3.0 + - - +
31X ILE* 3.4 27.3 - - + -
32X ILE* 3.0 23.6 + - - +
63X TYR* 5.5 0.2 - - + -
100X VAL* 3.7 26.0 - - + -
113X LEU* 3.8 28.3 - - + -
11Y PHE* 3.8 25.6 - - + -
98Y LEU* 4.8 12.8 - - + -
99Y VAL 3.6 4.9 - - - +
100Y VAL* 4.5 15.9 - - + -
112Y GLN* 1.3 77.7 - - - +
114Y GLU* 1.3 61.1 + - - +
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Residues in contact with GLU 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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32X ILE* 3.4 34.1 - - + +
33X ASN* 4.2 10.4 + - - +
62Y ARG* 5.8 1.6 + - - -
98Y LEU* 3.6 5.2 - - - -
99Y VAL* 2.6 60.0 + - + +
101Y ARG* 2.8 40.7 + - + +
112Y GLN 4.7 2.0 - - - +
113Y LEU* 1.3 78.8 - - - +
115Y LYS* 1.3 66.8 + - - +
116Y VAL* 3.6 8.9 + - - +
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Residues in contact with LYS 115 (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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31X ILE* 4.1 3.6 - - + +
32X ILE 2.9 11.2 + - - +
33X ASN* 3.4 38.0 + - - +
34X GLU* 2.6 33.5 + - + +
35X ASN 4.3 0.8 - - - -
36X GLN* 2.9 35.3 + - - +
37X ARG* 5.0 0.6 - - - +
63X TYR* 5.3 4.7 - - + +
96Y GLU* 3.0 41.5 + - + +
97Y THR 3.3 14.1 - - - +
98Y LEU* 3.9 14.6 - - + -
114Y GLU* 1.3 73.2 - - - +
116Y VAL* 1.3 62.5 + - - +
117Y LEU* 4.7 1.3 - - - -
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Residues in contact with VAL 116 (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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36X GLN* 5.0 2.0 - - - +
62Y ARG* 5.7 5.6 - - - +
67Y VAL* 4.5 13.5 - - + -
69Y GLN* 4.5 2.7 - - - +
97Y THR* 2.8 47.3 + - + +
99Y VAL* 3.6 41.3 - - + -
114Y GLU* 3.7 11.0 - - - +
115Y LYS* 1.3 79.0 - - - +
117Y LEU* 1.3 67.0 + - - +
118Y VAL* 3.9 20.6 - - + -
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Residues in contact with LEU 117 (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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36X GLN* 3.2 49.6 + - + +
37X ARG 3.1 28.3 - - - +
38X VAL* 4.0 9.0 - - + +
69Y GLN* 3.0 17.1 + - - +
94Y GLN* 3.5 26.6 + - - +
95Y GLN 3.6 2.5 - - - +
96Y GLU* 3.3 40.8 - - + +
115Y LYS* 4.7 1.8 - - - -
116Y VAL* 1.3 74.5 - - - +
118Y VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 118 (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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95X GLN* 3.6 33.7 - - - +
67Y VAL* 3.9 11.9 - - + -
68Y VAL 3.2 24.9 - - - +
69Y GLN* 3.2 12.3 - - - +
94Y GLN* 3.6 3.2 - - - -
95Y GLN 2.7 41.8 + - - +
97Y THR* 3.6 25.4 - - + -
116Y VAL* 3.9 7.4 - - + -
117Y LEU* 1.3 72.9 - - - +
119Y THR* 1.3 67.4 + - - +
120Y VAL* 3.2 7.3 + - + +
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Residues in contact with THR 119 (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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54Y TYR* 5.4 0.3 - - - -
68Y VAL 4.2 1.0 - - - +
69Y GLN* 2.8 18.1 + - - -
70Y ALA* 2.8 67.9 + - + +
71Y GLN* 4.9 1.1 - - - -
92Y PRO* 4.2 24.7 - - + +
93Y ILE 3.5 6.1 - - - +
94Y GLN* 3.7 19.0 + - - +
117Y LEU 4.1 0.6 + - - -
118Y VAL* 1.3 75.1 - - - +
120Y VAL* 1.3 56.3 + - - +
121Y GLY 4.1 6.3 - - - +
122Y CYS* 5.5 0.7 - - - -
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Residues in contact with VAL 120 (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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93X ILE* 3.5 29.3 - - + +
94X GLN 3.9 9.0 - - - +
95X GLN* 3.5 32.5 - - + +
120X VAL* 3.9 12.6 - - + -
40Y MET* 6.2 0.7 - - + -
52Y TRP* 4.0 0.5 + - - -
54Y TYR* 3.9 20.2 + - - -
70Y ALA* 3.8 4.2 - - - +
93Y ILE* 3.0 11.7 + - + +
95Y GLN* 3.5 32.8 - - + +
118Y VAL* 3.5 8.3 - - - +
119Y THR* 1.3 72.8 - - - +
121Y GLY* 1.3 56.7 + - - +
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Residues in contact with GLY 121 (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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93X ILE* 4.6 6.2 - - - +
52Y TRP* 3.7 21.5 - - - -
70Y ALA* 3.8 8.1 - - - -
92Y PRO* 3.5 3.3 - - - +
93Y ILE* 2.6 37.9 + - - +
119Y THR* 3.4 3.9 + - - +
120Y VAL* 1.3 80.7 - - - +
122Y CYS* 1.3 59.6 + - - -
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Residues in contact with CYS 122 (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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93X ILE* 4.2 0.6 - - - +
123X THR* 3.1 16.1 + - - -
50Y SER* 3.1 24.3 + - - +
52Y TRP* 3.2 24.4 - - - -
71Y GLN* 5.0 0.9 - - - -
72Y CYS* 2.0 64.8 - - + -
91Y VAL 3.2 6.3 - - - +
92Y PRO* 4.1 2.7 - - - -
93Y ILE* 4.4 5.2 - - - +
119Y THR* 5.5 1.1 - - - -
121Y GLY* 1.3 80.2 - - - -
123Y THR* 1.3 63.3 + - - +
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Residues in contact with THR 123 (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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44X ILE* 3.9 20.4 - - + -
48X SER* 2.8 20.4 + - - +
49X THR* 5.3 0.2 + - - -
50X SER* 3.8 0.3 + - - -
52X TRP* 4.2 1.6 - - + -
122X CYS 2.7 27.3 + - - -
123X THR* 3.8 7.3 - - - -
50Y SER* 2.8 15.1 + - - -
91Y VAL* 3.0 48.9 + - + -
93Y ILE* 3.7 10.4 - - - +
122Y CYS* 1.3 73.1 - - - +
124Y CYS* 1.3 59.2 + - - +
125Y VAL* 3.9 8.3 - - + -
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Residues in contact with CYS 124 (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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48X SER* 3.2 3.7 + - - -
49X THR* 2.8 52.1 + - + +
123X THR* 5.3 1.2 + - - +
124X CYS 5.4 0.8 - - - +
49Y THR* 3.4 21.1 - - - +
50Y SER* 3.2 3.7 + - - +
77Y CYS* 2.0 46.9 - - + -
88Y MET* 3.8 15.0 - - - -
89Y ASN 3.3 3.6 - - - -
123Y THR* 1.3 76.5 + - - +
125Y VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 125 (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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41X SER* 5.1 1.3 - - - +
44X ILE* 3.5 35.7 - - + -
47X ARG* 3.1 44.9 - - + +
48X SER* 4.1 1.3 - - - -
88Y MET* 3.6 4.0 - - - +
89Y ASN* 2.8 44.6 + - + +
91Y VAL* 3.7 26.0 - - + -
123Y THR* 3.9 3.6 - - + -
124Y CYS* 1.3 75.6 - - - +
126Y THR* 1.3 69.9 + - - +
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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