Contacts of the strand formed by residues 113 - 121 (chain A) in PDB entry 4NAM
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A PHE* 4.4 12.3 - - + -
69A ILE 3.6 3.8 - - - +
70A LYS* 3.6 32.8 - - + +
92A ASP* 4.7 3.3 - - - +
111A GLY 5.9 0.4 - - - +
112A ARG* 1.3 86.2 + - - +
114A TYR* 1.3 64.1 - - - +
115A GLN* 4.3 0.3 + - - +
152A GLN* 3.9 18.4 - - - +
163A SER* 3.5 31.4 - - - +
164A ARG* 3.5 35.7 - - + -
465A GLU* 4.6 8.1 - - - +
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Residues in contact with TYR 114 (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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68A PHE* 3.1 5.7 - - - -
69A ILE* 2.8 54.5 + - + +
71A VAL* 3.6 26.7 - - + -
91A VAL* 3.8 23.3 - - + -
92A ASP* 3.6 18.6 - - - +
106A ILE* 5.9 0.7 - - + -
107A ARG 4.5 2.9 + - - -
108A LEU* 3.4 19.8 - - + -
109A GLU* 2.7 36.8 + - - +
112A ARG* 3.7 50.0 + - + -
113A LEU* 1.3 76.6 - - - +
115A GLN* 1.3 62.0 + - - +
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Residues in contact with GLN 115 (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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67A GLY 3.5 8.2 + - - +
68A PHE* 3.5 20.7 - - + -
90A FTR 3.6 0.6 - - - +
91A VAL* 3.4 7.6 - - - -
92A ASP* 2.9 48.4 + - - +
113A LEU 4.3 0.2 + - - -
114A TYR* 1.3 73.8 - - - +
116A ILE* 1.3 63.9 + - - +
165A LYS* 3.8 37.0 + - + +
167A ARG 3.1 24.3 + - - +
168A SER* 3.8 11.4 + - - +
169A THR* 3.7 21.9 + - + +
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Residues in contact with ILE 116 (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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19A LEU* 4.3 17.7 - - + -
65A FTR 5.0 2.2 - - - +
66A SER* 3.4 6.9 + - - -
67A GLY 2.8 35.3 + - - +
68A PHE 4.0 2.7 - - - -
69A ILE* 3.7 44.9 - - + +
79A PHE* 5.2 1.1 - - + -
89A MET* 4.0 22.9 - - + -
90A FTR 3.6 1.1 - - - -
91A VAL* 4.1 12.3 - - + -
115A GLN* 1.3 82.8 - - - +
117A LYS* 1.3 63.3 + - - +
118A ILE* 3.9 29.8 - - + -
134A LEU* 5.1 2.9 - - + -
151A LEU* 5.5 2.2 - - + -
168A SER* 5.3 2.5 + - - -
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Residues in contact with LYS 117 (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 ILE* 4.8 8.1 - - + -
65A FTR 3.4 9.2 - - - +
66A SER* 5.6 2.5 - - - +
89A MET* 3.3 2.9 - - - +
90A FTR 2.9 52.6 + - + +
116A ILE* 1.3 74.4 - - - +
118A ILE* 1.3 67.7 + - - +
168A SER* 4.0 24.7 - - - +
169A THR* 2.9 34.9 + - + +
171A ALA 2.9 20.4 + - - +
172A GLY* 3.8 2.3 + - - -
173A PRO* 2.7 44.1 + - - -
174A THR* 4.4 5.9 + - - +
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Residues in contact with ILE 118 (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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19A LEU* 4.4 8.3 - - + -
43A LEU* 4.7 6.7 - - + -
63A ALA 4.0 0.2 - - - +
64A ILE* 3.2 8.0 - - - +
65A FTR 2.9 65.6 + - + +
81A THR* 5.1 1.3 - - + -
87A VAL* 4.1 22.0 - - + -
88A THR 3.5 3.4 - - - -
89A MET* 3.7 21.1 - - + -
90A FTR 3.7 2.2 - - - -
116A ILE* 3.9 19.1 - - + -
117A LYS* 1.3 80.8 - - - +
119A GLN* 1.3 61.2 + - - +
132A PHE* 4.3 7.9 - - + -
134A LEU* 3.9 27.6 - - + -
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Residues in contact with GLN 119 (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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29A PHE* 4.1 8.3 - - + -
63A ALA 3.4 7.2 - - - +
64A ILE* 4.6 0.4 - - + +
65A FTR 4.2 2.0 - - - -
86A HIS 5.5 1.5 + - - +
87A VAL* 3.2 8.7 - - - +
88A THR* 2.9 46.9 + - - +
90A FTR 3.2 23.2 - - - -
118A ILE* 1.3 73.5 - - - +
120A TYR* 1.3 60.9 + - - +
121A GLN* 3.1 30.5 + - - +
172A GLY* 4.1 1.4 - - - -
173A PRO* 2.9 41.6 - - + +
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Residues in contact with TYR 120 (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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29A PHE* 3.8 0.9 - - - -
60A PHE* 4.2 14.6 + - + -
61A GLN 4.5 0.9 - - - -
62A SER* 3.1 7.8 - - - -
63A ALA* 2.9 46.5 + - + +
65A FTR 3.1 24.5 - - - -
83A ALA* 4.1 13.7 - - + -
86A HIS* 3.3 31.4 - - + -
87A VAL* 4.3 3.1 - - + -
119A GLN* 1.3 71.8 - - - +
121A GLN* 1.3 70.0 + - - +
122A ARG* 2.9 46.0 + - + +
125A PRO* 5.5 1.0 - - - +
130A LEU* 3.8 31.8 - - + +
132A PHE* 4.0 18.8 - + + -
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Residues in contact with GLN 121 (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* 3.1 38.9 + - + +
28A ASN* 3.8 14.3 - - - +
29A PHE* 3.7 24.5 - - + -
61A GLN 3.3 4.7 - - - -
62A SER* 4.2 0.2 - - - -
86A HIS* 3.0 35.2 + - - +
119A GLN* 3.1 19.4 + - - +
120A TYR* 1.3 80.4 - - - +
122A ARG* 1.3 61.0 + - - +
123A GLU 4.4 0.2 - - - -
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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