Contacts of the strand formed by residues 121 - 128 (chain A) in PDB entry 1J7H
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 LEU 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.9 0.7 - - - +
35A PRO* 3.3 25.9 - - + +
47A ILE* 4.4 5.6 - - + +
50A GLN* 3.4 36.6 - - + +
51A ALA* 3.7 20.6 - - + +
54A SER* 3.3 30.5 - - - +
77A VAL* 4.9 6.7 - - + -
78A PHE 3.1 14.4 - - - +
79A VAL* 5.0 4.9 - - + -
88A VAL* 5.7 4.0 - - + -
115A LEU* 3.4 5.4 - - - +
119A VAL* 3.1 11.7 + - - +
120A GLY* 1.3 80.8 - - - +
122A GLU* 1.3 60.3 + - - +
123A ILE* 4.1 9.4 - - + -
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLY* 2.5 33.6 - - - +
33A GLN 3.2 10.1 - - - +
34A ILE* 3.4 10.2 - - + +
77A VAL* 2.7 35.5 - - - +
78A PHE* 3.0 15.2 + - + -
115A LEU* 3.5 14.4 - - + -
116A PRO* 3.5 17.6 - - - +
121A LEU* 1.3 75.6 - - - +
123A ILE* 1.3 62.7 + - - +
124A GLU* 3.4 15.0 - - - +
108C SER* 5.8 0.7 - - - -
109C CYS 3.5 9.1 + - - +
110C VAL* 3.1 28.1 - - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR* 5.0 0.2 - - - -
31A SER 2.8 4.2 - - - +
32A GLY* 3.1 0.9 - - - -
33A GLN* 2.6 34.6 + - + +
51A ALA 4.7 1.8 - - - +
54A SER* 2.9 50.3 - - - +
55A LEU* 3.7 20.9 - - + +
58A VAL* 3.4 28.3 - - + -
75A THR* 4.8 7.6 - - + -
76A THR 3.6 6.5 - - - +
77A VAL* 4.1 15.3 - - + -
92A TYR* 6.2 0.7 - - + -
121A LEU* 4.1 6.7 - - + -
122A GLU* 1.3 84.1 - - - +
124A GLU* 1.3 67.5 + - - +
125A ALA* 4.9 0.7 - - + +
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR* 3.7 18.4 - - - +
31A SER* 5.0 0.2 - - - -
32A GLY* 3.5 16.8 - - - +
75A THR 3.7 0.2 - - - -
76A THR* 2.8 55.8 + - + +
78A PHE* 2.8 49.9 - - + -
122A GLU* 3.4 12.0 - - - +
123A ILE* 1.3 77.7 - - - +
125A ALA* 1.3 59.1 + - - +
126A ILE* 5.6 1.3 - - - +
74C LYS* 5.6 5.6 - - - -
108C SER* 3.1 20.4 + - - +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR* 3.0 41.3 + - + +
58A VAL* 5.1 6.7 - - + -
62A ILE* 6.0 0.9 - - + -
72A ILE* 3.8 14.4 - - + -
74A LYS 3.0 20.0 - - - +
75A THR* 3.2 26.2 - - + +
123A ILE* 4.3 1.9 - - + +
124A GLU* 1.3 74.6 - - - +
126A ILE* 1.3 63.9 - - - +
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.5 24.0 - - + -
28A VAL 2.9 22.4 - - - +
29A LEU* 3.7 31.4 - - + -
30A THR* 4.9 2.7 - - - +
62A ILE* 6.2 0.4 - - - -
72A ILE* 3.0 13.4 - - - +
73A VAL* 2.8 33.9 + - + -
74A LYS* 2.7 25.2 + - + +
124A GLU 5.6 0.9 - - - -
125A ALA* 1.3 83.9 - - - +
127A ALA* 1.3 63.6 + - - +
29B LEU* 6.4 1.8 - - + -
74C LYS* 5.7 8.7 - - - +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.3 5.1 - - - +
28A VAL* 2.6 61.0 + - + +
30A THR* 6.0 0.4 - - + -
62A ILE* 4.3 18.6 - - + -
67A LEU* 4.5 3.1 - - + -
68A THR 4.8 0.2 - - - +
71A ASP* 4.3 2.9 - - + -
72A ILE* 3.8 23.1 - - + +
73A VAL 3.9 0.9 - - - +
126A ILE* 1.3 76.3 - - - +
128A VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASN 3.2 8.5 - - - +
27A LEU* 3.1 26.5 - - + -
67A LEU* 2.8 24.8 - - - +
71A ASP* 3.1 23.9 + - - +
73A VAL* 3.0 34.5 - - + -
127A ALA* 1.3 73.3 - - - +
129A ARG* 1.3 62.7 + - - +
130A LYS* 4.7 5.6 - - + +
3B THR* 3.5 21.5 - - + -
24B LEU* 3.6 17.7 - - + -
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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