Contacts of the helix formed by residues 162 - 171 (chain D) 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 GLY 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186C ARG 3.6 10.8 - - - -
187C LEU* 3.3 25.7 - - - +
188C TYR 5.4 0.4 - - - -
89D LEU* 4.4 4.7 - - - +
160D GLY* 4.5 0.4 - - - -
161D THR* 1.3 83.0 + - - +
163D PHE* 1.3 59.2 + - - +
164D PRO* 3.6 2.5 - - - -
165D HIS* 3.7 8.5 - - - -
166D ILE* 3.0 28.0 + - - +
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ILE* 3.2 42.8 - - + -
89D LEU* 3.9 12.1 - - + +
94D ILE* 4.8 3.8 - - + -
97D MET* 3.5 44.2 - - + -
120D LEU* 4.1 13.0 - - + -
121D PRO* 3.3 43.7 - - + +
159D PHE* 3.5 21.3 + - + +
160D GLY* 5.1 0.9 - - - +
161D THR 3.6 0.6 - - - +
162D GLY* 1.3 74.9 - - - +
164D PRO* 1.4 73.8 - - + +
166D ILE* 3.3 5.5 - - + +
167D LEU* 3.1 40.4 + - + +
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Residues in contact with PRO 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 3.9 22.0 - - + -
121D PRO 3.6 18.2 - - - +
122D ILE* 3.9 33.0 - - + -
136D TYR* 3.6 32.1 - - + -
161D THR 4.5 1.3 - - - +
162D GLY 3.8 1.1 - - - -
163D PHE* 1.4 97.7 - - + +
165D HIS* 1.3 62.3 + - + +
167D LEU* 3.4 6.0 + - + +
168D PHE* 3.1 28.7 - - - -
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Residues in contact with HIS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C PHE* 3.9 21.3 - + - -
185C PRO* 3.4 32.7 - - + +
186C ARG 3.7 16.6 + - - -
187C LEU* 4.4 7.4 - - + -
192C ILE* 3.6 23.7 - - + +
197C TYR* 4.9 2.4 + - - -
200C GLN* 4.9 1.4 + - - -
122D ILE* 4.4 5.6 - - + +
136D TYR* 4.3 20.2 + + - -
161D THR 3.2 27.1 + - - -
162D GLY* 3.7 11.4 - - - +
163D PHE 3.1 0.2 - - - -
164D PRO* 1.3 80.6 - - + +
166D ILE* 1.3 60.2 + - - +
167D LEU 3.4 0.7 + - - -
168D PHE* 3.5 4.9 + - - +
169D MET* 3.2 27.1 + - - +
175D ARG* 5.4 4.1 + - - +
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Residues in contact with ILE 166 (chain D).
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* 6.3 0.7 - - + -
47B ARG* 3.4 31.2 - - - +
52B GLU* 4.9 2.2 - - + -
54B PHE* 4.1 22.2 - - + -
187C LEU* 4.0 5.8 - - + -
188C TYR* 4.3 25.6 - - + +
88D ILE 4.9 0.4 - - - +
89D LEU* 3.9 22.2 - - + +
94D ILE* 4.2 13.8 - - + +
162D GLY 3.0 16.8 + - - +
163D PHE* 3.3 11.9 - - - +
165D HIS* 1.3 74.3 - - - +
167D LEU* 1.3 67.2 + - - +
169D MET* 3.3 17.5 + - + +
170D VAL* 3.3 19.1 + - + +
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 3.7 33.4 - - + +
98D LEU* 4.2 26.9 - - + +
101D TYR* 6.2 0.9 - - + -
120D LEU* 3.9 17.5 - - + -
163D PHE* 3.1 41.2 + - + +
164D PRO* 3.5 7.0 - - + +
165D HIS 3.2 0.2 - - - -
166D ILE* 1.3 80.6 - - + +
168D PHE* 1.3 84.7 + - + +
169D MET 3.2 0.4 - - - -
170D VAL* 3.3 10.9 - - - +
171D HIS* 2.9 35.6 + - + +
174D TYR* 5.2 1.1 - - + -
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Residues in contact with PHE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C GLN* 3.3 28.2 + - - +
101D TYR* 4.8 6.1 - + - -
120D LEU* 3.9 20.2 - - + -
136D TYR* 4.5 4.9 - + - -
138D PRO* 3.4 35.2 - - + -
164D PRO 3.1 25.2 + - - -
165D HIS 3.5 2.6 + - - +
166D ILE 3.4 0.2 - - - -
167D LEU* 1.3 83.5 - - + +
169D MET* 1.3 63.3 + - - +
170D VAL 3.4 0.2 - - - -
171D HIS 3.5 13.0 - - - -
172D PRO* 3.3 22.3 - - - +
174D TYR* 3.3 33.4 - - + -
175D ARG* 3.5 39.7 - - + +
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Residues in contact with MET 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.3 24.0 - - + -
42B VAL 3.9 24.2 - - - +
43B ARG* 4.2 2.3 - - - +
44B LYS* 4.0 39.7 + - + +
54B PHE* 3.9 13.7 - - + -
187C LEU* 4.5 6.1 - - + -
192C ILE* 4.4 17.3 - - + -
196C ALA* 4.4 11.7 - - + -
200C GLN* 4.3 9.9 - - - +
165D HIS 3.2 18.3 + - - +
166D ILE* 3.4 17.7 - - + +
167D LEU 3.2 0.6 - - - -
168D PHE* 1.3 80.5 - - - +
170D VAL* 1.3 61.2 + - + +
172D PRO* 3.9 9.9 - - - +
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Residues in contact with VAL 170 (chain D).
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* 3.7 37.3 + - + +
47B ARG* 4.8 8.5 - - - +
91D ASN* 4.4 17.0 - - - +
94D ILE* 4.0 18.8 - - + -
166D ILE* 3.6 13.9 - - + +
167D LEU 3.3 11.4 - - - +
169D MET* 1.3 77.9 - - + +
171D HIS* 1.3 93.3 + - + +
172D PRO* 3.5 7.3 - - - +
173D GLU* 4.6 0.5 - - - +
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Residues in contact with HIS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ASN 5.6 2.9 - - - -
94D ILE* 3.9 16.9 - - + +
95D ALA* 5.2 7.0 - - + -
98D LEU* 3.6 27.3 - - + +
167D LEU* 2.9 16.8 + - + +
168D PHE* 3.5 19.5 - - - -
170D VAL* 1.3 114.4 - - + +
172D PRO* 1.3 60.2 - - - +
173D GLU* 3.1 27.1 + - - +
174D TYR* 3.4 17.9 + + + +
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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