Contacts of the strand formed by residues 106 - 112 (chain B) in PDB entry 3NVN
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 SER 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B GLY* 4.3 8.2 - - - +
48B ALA* 3.3 23.9 - - - +
60B ALA* 3.6 26.7 - - - +
61B SER 5.6 1.5 + - - -
62B GLY 4.8 3.7 + - - -
104B SER* 2.8 23.5 + - - -
105B PHE* 1.3 78.3 - - - +
107B LYS* 1.3 62.1 + - - +
108B LEU 4.2 7.1 + - - -
109B LEU* 5.0 1.6 - - - +
126B GLY 3.9 4.6 + - - -
127B TRP* 3.4 17.7 + - - -
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Residues in contact with LYS 107 (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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48B ALA* 5.8 2.5 - - - -
103B SER* 5.3 0.2 - - - +
104B SER* 3.3 13.9 + - - +
105B PHE 3.7 0.2 + - - -
106B SER* 1.3 76.6 - - - +
108B LEU* 1.3 62.9 + - - +
126B GLY 3.1 7.3 + - - +
127B TRP 4.2 2.9 - - - -
128B THR* 3.5 16.8 - - + -
154B VAL* 3.1 34.3 - - + -
155B SER 3.8 6.3 - - - +
157B HIS 3.0 22.7 - - - -
158B PRO 2.7 24.0 + - - -
159B GLN 4.3 0.4 - - - -
160B GLY 2.7 26.8 + - - +
162B THR* 3.6 36.6 - - - +
163B ALA* 5.5 0.5 - - - -
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Residues in contact with LEU 108 (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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48B ALA* 5.4 0.7 - - - -
106B SER* 3.8 5.0 + - - -
107B LYS* 1.3 83.0 - - - +
109B LEU* 1.3 62.1 + - - +
110B LEU* 3.3 35.9 - - + -
124B LEU* 3.7 24.2 - - + +
125B THR* 3.5 4.2 - - - -
126B GLY* 2.8 38.6 + - - +
134B CYS* 4.5 6.7 - - - -
153B VAL* 5.1 0.2 - - + -
154B VAL* 3.8 22.0 - - + -
162B THR* 4.6 3.1 - - + -
164B GLY* 4.7 8.1 - - - +
177B LEU* 4.4 24.2 - - + -
179B VAL* 4.4 12.8 - - + -
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Residues in contact with LEU 109 (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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48B ALA* 4.0 30.5 - - + +
49B ILE 5.2 0.4 - - - +
50B ALA* 3.6 31.3 - - + +
58B PHE* 3.5 34.1 - - + +
60B ALA* 4.8 1.1 - - + -
65B LEU* 3.8 27.8 - - + -
106B SER* 5.0 1.1 - - - +
108B LEU* 1.3 78.3 - - - +
110B LEU* 1.3 72.2 + - - +
111B PRO* 3.8 0.8 - - - +
123B LEU* 4.2 12.1 - - + -
124B LEU 3.4 1.1 - - - -
125B THR* 4.1 22.0 - - + -
127B TRP* 6.4 0.2 - - + -
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Residues in contact with LEU 110 (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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108B LEU* 3.3 26.5 - - + -
109B LEU* 1.3 84.9 - - - +
111B PRO* 1.3 67.9 - - + +
112B TYR* 3.6 5.9 + - + -
123B LEU* 3.6 4.9 - - - +
124B LEU* 2.9 39.9 + - + +
164B GLY 3.2 36.6 - - - +
165B VAL* 3.9 11.4 - - - +
166B VAL* 4.5 7.2 - - + +
177B LEU* 4.0 13.0 - - + -
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Residues in contact with PRO 111 (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 ALA* 4.0 20.0 - - + -
51B ALA 4.7 3.1 - - - +
52B SER* 4.6 15.0 - - - +
58B PHE* 5.1 2.9 - - + -
109B LEU 3.8 7.2 - - - +
110B LEU* 1.3 87.2 - - + +
112B TYR* 1.3 61.9 + - - +
114B GLU* 3.8 30.0 - - - +
122B LEU 3.6 7.0 - - - +
123B LEU* 3.8 15.3 - - + -
139B LEU* 4.0 11.9 - - + -
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Residues in contact with TYR 112 (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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110B LEU* 3.7 11.0 - - + +
111B PRO* 1.3 75.1 - - - +
113B ARG* 1.3 99.2 + - + +
114B GLU* 3.3 8.5 + - - +
121B GLY* 3.8 0.9 - - - -
122B LEU* 2.8 72.9 + - + +
123B LEU 4.1 1.3 - - - -
124B LEU* 3.6 26.5 - - + -
136B VAL* 3.6 14.0 - - + +
139B LEU* 4.5 0.2 - - - +
148B ARG* 4.7 0.3 + - - -
166B VAL* 3.8 25.4 - - + -
175B TRP* 3.7 28.0 - + + -
210B THR* 3.7 24.5 - - + +
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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