Contacts of the strand formed by residues 96 - 108 (chain A) in PDB entry 1NNF
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 ILE 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.9 6.3 - - + -
78A THR* 3.4 33.9 - - + +
79A ILE* 3.7 18.2 - - + +
82A THR* 3.5 14.1 - - - +
95A TRP* 1.3 84.3 - - - +
97A ALA* 1.3 71.4 + - - +
98A LEU* 4.1 12.3 - - + -
229A GLY* 3.0 4.9 - - - -
230A ALA* 2.9 44.0 + - + +
246A VAL* 3.6 24.0 - - + -
250A ALA* 3.9 17.0 - - + -
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Residues in contact with ALA 97 (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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59A THR* 4.1 12.6 - - + -
82A THR* 2.7 30.7 + - - +
87A VAL* 3.6 28.3 - - + -
88A PRO* 3.8 13.0 + - + +
95A TRP* 3.9 5.3 - - + -
96A ILE* 1.3 77.4 - - - +
98A LEU* 1.3 58.6 + - - +
227A TYR* 4.4 9.0 - - + -
228A SER 3.5 8.7 - - - +
267A LEU* 3.7 7.2 - - + -
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Residues in contact with LEU 98 (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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55A TYR* 4.1 10.1 - - + -
82A THR* 4.5 2.0 - - + -
96A ILE* 3.9 16.4 - - + +
97A ALA* 1.3 79.7 - - - +
99A SER* 1.3 63.3 + - - +
228A SER* 2.8 14.4 + - - +
229A GLY* 3.9 9.2 - - - -
230A ALA* 3.9 16.2 - - + -
246A VAL 5.0 0.2 - - - +
249A LEU* 3.7 57.9 - - + +
250A ALA* 3.9 15.7 - - + +
255A GLN* 2.9 26.8 + - - +
258A LEU* 6.3 1.6 - - + -
267A LEU* 3.3 19.6 + - - +
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Residues in contact with SER 99 (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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8A GLN* 4.9 0.2 + - - -
98A LEU* 1.3 82.2 - - - +
100A GLY* 1.3 59.5 + - - +
227A TYR* 3.3 8.0 - - - +
228A SER* 2.8 33.0 + - - +
255A GLN* 5.3 0.4 - - - -
258A LEU* 3.9 22.4 - - - +
264A GLU* 2.6 32.9 + - - +
265A TYR 3.0 16.6 - - - -
266A PRO* 4.5 0.9 - - - -
267A LEU* 3.5 9.9 - - - +
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Residues in contact with GLY 100 (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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99A SER* 1.3 75.9 - - - +
101A ARG* 1.3 64.4 + - - -
225A VAL* 3.8 14.4 - - - -
226A SER 3.2 9.9 - - - -
227A TYR* 4.4 1.8 - - - -
264A GLU* 3.2 9.3 - - - -
265A TYR* 2.8 42.5 + - - -
267A LEU* 4.6 1.9 - - - +
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Residues in contact with ARG 101 (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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8A GLN* 4.8 0.2 + - - -
57A GLU* 2.8 29.3 + - - +
58A GLN* 4.9 2.4 - - - +
100A GLY* 1.3 74.7 - - - +
102A SER* 1.3 61.1 + - - +
103A ARG 4.3 0.2 + - - -
193A ASN* 5.4 2.5 - - + -
194A ASN* 3.7 4.9 - - - +
195A TYR* 3.6 25.9 - - + -
224A LEU 3.9 0.2 - - - +
225A VAL* 3.2 5.3 - - - -
226A SER* 2.8 62.1 + - - +
228A SER* 2.9 28.1 + - - -
262A ARG* 3.5 22.9 - - - +
264A GLU* 3.0 31.9 + - + +
400A EDT 3.5 28.0 + - - -
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Residues in contact with SER 102 (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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101A ARG* 1.3 74.6 - - - +
103A ARG* 1.3 77.7 + - - +
193A ASN* 3.2 7.1 - - - -
194A ASN* 2.8 38.4 + - - +
215A PHE* 3.8 18.5 - - - -
223A ALA* 4.3 5.9 + - - -
224A LEU 3.6 8.1 + - - -
225A VAL* 4.2 12.8 - - - +
265A TYR* 3.8 21.0 - - - -
283A LEU* 4.3 6.0 - - - +
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Residues in contact with ARG 103 (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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102A SER* 1.3 89.5 + - - +
104A VAL* 1.3 61.6 - - - +
139A SER* 4.4 3.8 + - - -
141A ALA* 3.5 33.2 + - - +
142A PHE* 3.8 26.2 - - - +
145A GLN* 3.9 26.0 + - - +
161A TRP* 5.4 0.2 - - - -
175A ASN* 4.6 2.6 + - - -
191A LEU* 3.8 31.9 + - - +
192A ILE* 3.5 18.8 + - - +
193A ASN* 2.9 24.8 + - - +
215A PHE* 4.3 4.0 - - - -
222A GLY* 3.5 24.8 - - - +
223A ALA* 5.1 0.5 - - - -
224A LEU* 3.0 33.4 + - + +
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Residues in contact with VAL 104 (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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103A ARG* 1.3 77.9 + - - +
105A VAL* 1.3 70.5 + - - +
191A LEU* 3.6 5.4 - - - +
192A ILE* 2.9 43.4 + - + +
193A ASN 3.6 25.8 - - - -
194A ASN* 3.7 5.2 - - - +
213A LEU* 3.8 31.2 - - + -
214A TYR 3.3 14.8 - - - +
215A PHE* 3.7 32.3 - - + +
222A GLY 5.1 2.2 - - - -
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Residues in contact with VAL 105 (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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104A VAL* 1.3 77.4 - - - +
106A VAL* 1.3 71.1 + - - +
117A MET* 4.2 19.7 - - - -
121A VAL* 5.6 3.1 - - + -
124A TYR* 3.7 39.3 - - + +
133A ILE* 4.6 0.4 - - + -
189A ALA* 4.2 9.0 - - + -
190A ALA 3.4 11.4 - - - +
191A LEU* 3.8 15.0 - - + -
213A LEU* 3.4 2.8 - - - -
214A TYR* 2.8 50.0 + - + +
216A VAL* 5.1 5.4 - - + -
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Residues in contact with VAL 106 (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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104A VAL* 4.0 1.4 + - - +
105A VAL* 1.3 74.3 - - - +
107A TYR* 1.3 62.1 + - - +
179A LEU* 3.8 19.1 - - + -
182A VAL* 4.0 11.4 - - + -
189A ALA* 3.0 5.0 - - - +
190A ALA* 2.8 56.2 + - + +
192A ILE* 3.7 24.0 - - + -
197A TRP* 3.9 9.2 - - + -
211A SER* 3.6 23.3 - - - -
212A ARG 3.3 12.3 - - - +
213A LEU* 3.8 9.4 - - + +
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Residues in contact with TYR 107 (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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106A VAL* 1.3 76.3 - - - +
108A ASP* 1.3 63.3 + - - +
109A HIS* 3.3 14.3 + - + +
112A LEU* 3.4 38.1 - - + -
113A SER* 4.1 5.3 - - - -
114A GLU* 3.4 30.7 + - + +
117A MET* 4.0 29.4 - - + -
182A VAL* 3.6 7.0 - - - -
188A PRO 3.2 11.4 - - - +
189A ALA* 4.1 4.3 - - + -
211A SER* 3.1 2.3 - - - -
212A ARG* 2.8 55.5 + - + +
213A LEU 3.7 23.4 + - - -
214A TYR* 3.9 13.0 - - + -
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Residues in contact with ASP 108 (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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107A TYR* 1.3 69.9 - - - +
109A HIS* 1.3 58.7 + - - +
110A THR* 2.6 27.9 + - - +
111A LYS* 3.0 28.1 + - + +
112A LEU* 2.9 26.5 + - - +
182A VAL* 3.5 19.5 - - + +
185A GLY* 4.4 1.0 - - - -
187A VAL 4.8 0.2 - - - +
188A PRO* 2.8 24.9 + - + +
210A LYS* 2.8 40.6 + - + +
211A SER* 4.3 1.1 - - - +
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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