Contacts of the strand formed by residues 39 - 47 (chain B) in PDB entry 4NH1
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 TYR 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASN 3.6 10.1 - - - -
36B GLN* 3.1 16.3 + - - +
37B ASP* 3.1 3.8 - - - +
38B ASP* 1.3 88.3 + - + +
40B GLN* 1.3 67.4 + - - +
56B ALA* 4.9 2.2 - - + -
57B ILE 4.2 2.5 - - - -
58B ASN* 3.2 37.2 + - + -
65B VAL* 4.3 14.1 - - + -
67B VAL* 4.7 7.9 - - + -
98B ALA* 5.3 1.2 - - - +
99B ASP* 3.3 25.7 + - - +
101B VAL* 3.5 28.5 - - + -
112B VAL* 3.7 29.5 - - + +
190C PHE* 3.7 35.9 - + + -
191C LYS* 3.8 9.9 + - - +
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Residues in contact with GLN 40 (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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37B ASP 5.2 0.4 - - - +
39B TYR* 1.3 79.6 - - - +
41B LEU* 1.3 64.8 + - - +
42B VAL* 3.7 3.3 - - - +
56B ALA* 3.2 4.9 - - - +
57B ILE 3.1 33.3 + - - +
59B ILE* 3.4 37.6 - - + +
191C LYS* 3.3 35.0 - - + +
192C ILE 4.0 1.9 - - - +
193C HIS* 3.3 42.1 + - + +
194C PRO* 4.1 4.0 - - - +
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Residues in contact with LEU 41 (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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40B GLN* 1.3 72.2 - - - +
42B VAL* 1.3 58.8 + - - +
54B PHE* 3.9 36.3 - - + -
55B GLU 4.0 2.7 - - - -
56B ALA* 4.1 8.7 - - + -
67B VAL* 4.6 7.4 - - + -
69B ILE* 4.9 2.0 - - + -
187C LEU* 3.7 52.3 - - + +
190C PHE* 3.6 31.4 - - + -
191C LYS 2.9 12.4 + - - +
192C ILE* 3.6 10.3 - - + +
193C HIS* 3.0 22.9 + - - +
196C ALA* 4.0 0.2 - - - +
169D MET* 4.3 13.5 - - + -
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Residues in contact with VAL 42 (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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40B GLN 3.7 4.7 - - - +
41B LEU* 1.3 80.2 - - - +
43B ARG* 1.3 62.2 + - + +
55B GLU* 2.8 28.5 + - + +
56B ALA* 4.1 0.4 - - - -
57B ILE* 3.6 33.7 - - + +
193C HIS* 3.7 15.3 - - + -
195C MET* 4.1 9.0 - - + -
196C ALA* 3.2 37.4 - - - +
199C LEU* 3.7 26.7 - - + +
200C GLN* 5.2 0.3 + - - -
169D MET* 3.9 9.8 - - - +
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Residues in contact with ARG 43 (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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42B VAL* 1.3 87.9 - - + +
44B LYS* 1.3 72.6 + - - +
45B LEU* 3.3 18.7 - - + +
54B PHE* 3.5 6.1 - - - -
55B GLU* 2.6 67.5 + - - +
115B HIS* 6.1 0.2 + - - -
199C LEU* 4.4 17.7 - - + -
169D MET* 4.2 5.7 - - - +
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Residues in contact with LYS 44 (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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43B ARG* 1.3 82.7 + - - +
45B LEU* 1.3 64.6 + - - +
46B GLY* 3.8 18.6 - - - +
47B ARG* 4.4 19.3 - - + +
52B GLU* 6.4 0.2 - - + -
53B VAL 3.8 9.6 - - - +
54B PHE* 3.8 28.3 - - + -
91D ASN* 5.7 0.8 + - - -
166D ILE* 6.3 0.4 - - + -
169D MET* 4.0 25.4 + - + +
170D VAL* 3.7 37.9 + - + +
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Residues in contact with LEU 45 (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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43B ARG* 3.3 37.2 + - - +
44B LYS* 1.3 75.5 - - - +
46B GLY* 1.3 59.4 + - - +
53B VAL* 3.2 15.5 + - + +
55B GLU* 3.6 34.1 - - + +
66B VAL* 3.8 24.0 - - + -
115B HIS* 4.9 3.8 - - + +
404B ACP 3.6 51.4 + - + +
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Residues in contact with GLY 46 (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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44B LYS* 3.4 14.3 - - - +
45B LEU* 1.3 82.5 - - - +
47B ARG* 1.3 59.4 + - - +
53B VAL* 2.7 42.5 + - - +
404B ACP 4.9 8.5 - - - -
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Residues in contact with ARG 47 (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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44B LYS* 4.4 21.1 - - + +
46B GLY* 1.3 74.7 - - - +
48B GLY* 1.3 59.3 + - - +
51B SER 3.6 6.7 - - - -
52B GLU* 3.0 46.7 + - + +
53B VAL* 4.3 2.0 - - - +
71B LYS* 5.1 4.6 - - - +
404B ACP 5.3 5.8 - - - +
188C TYR* 4.8 1.6 + - - -
89D LEU* 2.6 39.6 + - - +
90D THR* 4.1 11.7 - - - +
91D ASN* 4.1 30.6 + - - +
94D ILE* 4.7 3.4 - - - +
166D ILE* 3.4 22.0 - - - +
170D VAL* 4.8 3.5 - - - +
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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