Contacts of the strand formed by residues 76 - 84 (chain A) in PDB entry 1TNF
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.5 42.2 - - + -
74A VAL* 3.9 11.2 - - + -
75A LEU* 1.3 75.3 - - - +
77A THR* 1.3 58.1 + - - +
96A ALA 3.9 0.2 - - - +
97A ILE* 3.1 6.4 - - - +
98A LYS* 2.9 40.0 + - + +
100A PRO* 3.7 37.7 - - + -
114A TRP* 4.2 10.3 - - + -
116A GLU* 4.4 11.7 - - + -
118A ILE* 4.6 1.1 - - - -
137A ASN* 3.4 4.3 - - - -
138A ARG* 4.4 2.9 - - + -
141A TYR* 3.3 34.3 - - + -
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Residues in contact with THR 77 (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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64A PHE* 4.1 1.3 - - - -
75A LEU* 4.7 3.1 - - + +
76A LEU* 1.3 80.4 - - - +
78A HIS* 1.3 61.6 + - - +
79A THR* 4.8 9.4 + - - -
95A SER* 5.6 0.9 - - - -
96A ALA 3.3 6.3 - - - -
97A ILE* 3.5 27.1 - - + -
118A ILE* 4.4 2.0 - - - -
135A GLU 5.1 0.7 + - - -
136A ILE* 3.3 26.7 - - - +
137A ASN* 2.8 41.0 + - + +
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 5.1 0.2 - - - +
28A TRP* 5.8 0.2 - - - -
60A SER* 3.0 39.5 + - - -
61A GLN 4.7 0.4 - - - -
62A VAL* 3.8 21.7 - - + +
77A THR* 1.3 75.8 - - - +
79A THR* 1.3 61.4 + - - +
80A ILE* 4.9 1.6 - - + -
95A SER* 3.2 10.4 - - - -
96A ALA 2.9 12.4 + - - +
118A ILE* 3.7 36.2 + - + +
120A LEU* 3.0 36.8 - - + +
134A ALA* 4.1 14.8 + - - +
135A GLU 3.5 15.3 - - - -
136A ILE* 3.5 17.0 - - + -
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Residues in contact with THR 79 (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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77A THR* 4.3 8.2 + - - -
78A HIS* 1.3 74.3 + - - +
80A ILE* 1.4 63.3 + - - +
81A SER* 4.1 9.5 + - - +
92A ASN* 2.9 44.0 - - - +
94A LEU 3.3 6.7 - - - +
95A SER* 3.0 14.8 + - - +
133A SER 3.9 0.2 - - - +
134A ALA* 3.6 2.3 - - - -
135A GLU* 3.1 41.6 + - - +
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Residues in contact with ILE 80 (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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58A ILE* 3.9 22.9 - - + -
59A TYR 4.1 5.2 - - - +
60A SER* 3.5 31.9 - - - +
78A HIS* 4.9 0.9 - - + -
79A THR* 1.4 74.3 - - - +
81A SER* 1.3 54.8 + - - +
93A LEU* 2.7 35.8 + - + +
94A LEU* 2.9 39.1 + - + +
120A LEU* 4.1 13.9 - - + -
132A LEU* 4.3 7.0 - - + -
133A SER 3.3 15.0 - - - +
134A ALA* 4.3 7.9 - - + -
152A PHE* 3.7 17.9 - - + -
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Residues in contact with SER 81 (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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79A THR* 4.1 13.7 + - - +
80A ILE* 1.3 72.8 - - - +
82A ARG* 1.3 62.2 + - - +
90A LYS* 3.4 36.8 + - - +
91A VAL 3.1 16.8 + - - -
92A ASN* 4.2 4.4 + - - +
93A LEU* 4.0 5.6 - - - +
132A LEU* 3.4 9.5 - - - +
133A SER* 2.9 32.9 + - - -
135A GLU* 4.5 5.7 + - - -
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Residues in contact with ARG 82 (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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81A SER* 1.3 74.2 - - - +
83A ILE* 1.3 61.9 + - - +
84A ALA* 3.4 30.3 + - + +
87A TYR* 4.1 15.6 + - - -
89A THR 2.9 2.6 - - - +
90A LYS* 4.1 1.3 - - - -
91A VAL* 2.8 40.5 + - + +
93A LEU* 3.5 19.4 - - + +
124A PHE* 5.9 0.6 - - - +
125A GLN 4.2 13.5 + - - +
126A LEU* 3.3 33.9 - - - +
127A GLU* 4.7 6.9 - - - +
130A ASP* 2.9 29.6 + - - -
131A ARG 3.6 7.0 - - - +
132A LEU* 4.5 1.3 - - + -
34B ASN* 3.2 33.7 + - - +
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Residues in contact with ILE 83 (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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47A GLN* 3.7 25.4 - - - +
81A SER 5.5 0.2 - - - +
82A ARG* 1.3 73.8 - - - +
84A ALA* 1.4 59.5 + - - +
88A GLN* 4.4 16.1 - - + +
89A THR* 3.1 34.5 - - - +
90A LYS* 3.9 18.2 - - + +
130A ASP* 3.6 0.9 - - - +
131A ARG* 3.0 42.2 + - + +
133A SER* 4.4 9.4 - - - +
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Residues in contact with ALA 84 (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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82A ARG* 3.4 35.2 + - + +
83A ILE* 1.4 74.5 - - - +
85A VAL* 1.3 66.5 + - - +
86A SER* 3.0 2.1 + - - +
87A TYR* 3.7 30.5 - - + +
88A GLN* 3.0 30.6 - - - +
89A THR 3.6 4.6 + - - -
91A VAL* 6.4 1.1 - - + -
130A ASP* 3.3 8.1 - - - -
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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