Contacts of the strand formed by residues 112 - 126 (chain B) 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 LYS 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A THR* 3.0 26.6 + - - +
73A HIS* 3.3 38.4 - - + +
102A GLN* 3.6 20.0 + - - +
103A ARG* 3.7 43.0 - - + +
68B GLY* 2.8 21.3 + - - -
104B GLU* 4.7 4.5 - - - +
109B ALA* 5.8 1.4 + - - +
111B ALA* 1.3 85.3 - - - +
113B PRO* 1.3 64.8 - - + +
114B TRP 3.9 1.2 + - - -
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Residues in contact with PRO 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A HIS* 2.6 41.5 + - + +
75A LEU* 5.8 0.4 - - + -
99A SER* 4.3 1.4 - - - -
102A GLN* 4.4 0.7 - - - -
65B LYS* 5.9 3.6 - - + -
66B GLY 3.3 8.5 - - - +
67B GLN* 3.5 26.5 - - + +
111B ALA 3.9 4.9 - - - +
112B LYS* 1.3 88.5 - - + +
114B TRP* 1.3 62.1 + - - +
115B TYR* 4.4 17.4 - - + +
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Residues in contact with TRP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A SER* 3.5 15.5 - - - +
102A GLN* 3.1 29.6 - - - +
64B PHE* 3.9 21.1 - - + -
65B LYS* 3.4 21.5 - - - +
66B GLY* 3.0 34.1 + - - -
68B GLY 3.2 21.5 + - - -
69B CYS* 3.8 14.5 - - - -
74B VAL* 5.6 0.9 - - + -
76B LEU* 4.1 13.2 - - + -
100B PRO* 3.6 41.1 - - + +
101B CYS* 3.9 3.6 - - - -
112B LYS 4.4 1.1 - - - -
113B PRO* 1.3 74.3 - - - +
115B TYR* 1.3 77.0 + - - +
116B GLU* 3.9 16.4 - - + +
141B TYR* 4.3 20.9 - + - -
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.3 35.1 - - + +
97A ILE* 3.6 50.1 - - + +
98A LYS* 4.5 0.9 - - - +
99A SER* 3.6 23.0 + - - +
63B LEU* 4.3 11.9 - - + -
64B PHE 3.3 7.4 - - - -
65B LYS* 3.6 28.9 - - + +
113B PRO* 4.5 15.5 - - + +
114B TRP* 1.3 80.4 - - - +
116B GLU* 1.3 75.2 + - - +
117B PRO* 4.3 3.8 - - - +
143B LEU* 4.3 14.4 - - + +
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LYS* 4.6 5.7 - - - +
99A SER* 5.0 3.2 + - - +
116A GLU* 5.2 2.6 - - - +
63B LEU* 3.9 1.5 - - - +
64B PHE* 3.0 31.9 + - + +
76B LEU* 4.0 14.6 - - + -
98B LYS* 3.3 47.2 + - + +
99B SER 4.8 0.6 - - - +
100B PRO* 3.3 28.9 - - + +
114B TRP* 3.9 20.1 - - + +
115B TYR* 1.3 85.0 - - - +
117B PRO* 1.3 61.0 - - - +
118B ILE* 5.3 0.4 - - + -
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Residues in contact with PRO 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ALA* 4.3 18.2 - - + -
97A ILE 3.5 23.3 - - - +
98A LYS* 3.7 24.0 - - + -
118A ILE* 5.6 4.0 - - + -
61B GLN* 4.9 10.1 - - + +
62B VAL 3.4 9.4 - - - +
63B LEU* 4.0 14.4 - - + -
98B LYS* 3.1 29.3 + - - +
116B GLU* 1.3 82.4 - - - +
118B ILE* 1.3 62.2 + - - +
119B TYR 4.4 0.2 - - - -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B SER 3.3 2.1 - - - +
61B GLN* 3.3 24.4 - - - +
62B VAL* 2.9 18.8 + - + -
64B PHE* 4.1 24.5 - - + -
76B LEU* 4.4 7.6 - - + +
78B HIS* 3.5 30.3 + - + +
96B ALA* 3.3 33.0 - - + +
97B ILE 4.7 0.2 - - - -
98B LYS* 3.8 39.7 - - + +
116B GLU* 5.2 0.9 - - + +
117B PRO* 1.3 80.2 - - - +
119B TYR* 1.3 66.8 + - - +
120B LEU* 4.3 0.4 - - + -
117C PRO* 4.9 4.5 - - + -
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Residues in contact with TYR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A TYR* 4.5 24.9 - + + +
120A LEU 4.4 1.6 - - - -
121A GLY* 2.8 32.5 + - - -
57B LEU* 5.9 0.2 - - - +
59B TYR* 3.4 20.1 - - + +
60B SER 3.3 3.8 - - - -
61B GLN* 4.1 15.5 - - + +
118B ILE* 1.3 77.1 - - - +
120B LEU* 1.3 106.5 + - - +
121B GLY* 3.8 7.9 - - - -
151B TYR* 3.3 30.7 - + - -
61C GLN* 3.9 9.0 + - - -
119C TYR* 3.9 39.7 - + + +
151C TYR* 4.5 0.3 + - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.0 2.8 - - - -
60B SER* 2.7 42.9 + - - +
78B HIS* 3.5 38.8 - - + +
79B THR* 4.0 6.1 - - - -
80B ILE* 3.9 18.8 - - + -
94B LEU* 3.6 24.2 - - + +
95B SER 3.7 19.7 - - - +
96B ALA* 3.8 8.3 - - + -
118B ILE* 4.3 1.8 - - + -
119B TYR* 1.3 91.5 - - - +
121B GLY* 1.3 56.8 + - - +
61C GLN* 3.5 20.4 - - - +
151C TYR* 4.0 3.4 - - - +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.8 5.6 - - - -
58B ILE 3.3 8.1 - - - -
59B TYR* 3.9 6.7 - - - -
94B LEU* 3.6 6.8 - - - +
119B TYR* 3.8 4.7 - - - -
120B LEU* 1.3 74.5 - - - +
122B GLY* 1.3 57.2 + - - -
59C TYR* 3.7 4.4 - - - -
119C TYR* 3.2 35.9 + - - -
151C TYR* 3.5 15.1 + - - -
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR 3.5 0.3 - - - +
57B LEU* 3.3 7.6 - - - +
58B ILE 2.9 34.3 + - - +
94B LEU* 3.9 4.9 - - - +
121B GLY* 1.3 73.9 - - - -
123B VAL* 1.3 62.4 + - - -
124B PHE* 3.5 18.8 - - - -
59C TYR* 3.6 17.7 - - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 4.1 13.2 - - + -
56B TYR 3.2 11.4 - - - +
57B LEU* 4.4 13.9 - - + -
122B GLY* 1.3 75.0 - - - +
124B PHE* 1.3 74.0 + - - +
157B LEU* 4.7 0.9 - - + -
13C VAL* 3.9 18.8 - - + -
14C ALA 5.1 0.9 - - - +
15C HIS* 3.6 16.4 - - + +
34C ASN* 3.4 7.2 - - - +
36C LEU* 5.9 0.4 - - - -
57C LEU* 5.3 0.7 - - + -
59C TYR* 2.7 32.2 + - + +
154C ILE 5.1 0.4 - - - +
155C ILE* 3.8 45.3 - - + -
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 4.0 4.7 - - - -
56B TYR* 2.7 43.2 + - - +
58B ILE* 3.8 25.1 - - + -
93B LEU* 3.7 39.7 - - + -
94B LEU* 3.4 32.8 - - + -
122B GLY* 3.5 30.5 - - - -
123B VAL* 1.3 81.4 - - - +
125B GLN* 1.3 63.4 + - - +
126B LEU* 3.5 4.7 + - + +
15C HIS* 3.8 26.0 - + - -
34C ASN* 3.2 34.8 - - + +
36C LEU* 5.6 0.2 - - - -
147C SER* 6.5 0.2 - - - -
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU* 3.2 25.5 + - - -
54B GLY 3.6 13.9 - - - +
55B LEU* 3.6 16.1 - - + +
82B ARG* 4.2 13.2 + - - -
124B PHE* 1.3 72.5 - - - +
126B LEU* 1.3 71.7 + - - +
127B GLU* 3.6 16.5 + - - +
6C ARG* 2.5 40.3 + - - +
8C PRO* 4.3 7.1 - - + +
34C ASN* 3.2 23.8 + - - +
36C LEU* 4.1 5.0 - - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 3.9 27.6 - - + -
53B GLU* 3.8 7.3 - - - +
54B GLY 3.5 10.6 + - - +
56B TYR* 3.4 37.7 - - + -
58B ILE* 3.9 21.3 - - + -
82B ARG* 3.7 22.7 - - + +
93B LEU* 4.9 3.1 - - + -
124B PHE* 3.5 7.6 + - + +
125B GLN* 1.3 86.9 - - - +
127B GLU* 1.3 73.0 + - - +
130B ASP* 3.3 16.8 - - + +
132B LEU* 3.7 24.9 - - + -
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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