Contacts of the strand formed by residues 137 - 148 (chain L) in PDB entry 5D4D
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 ARG 137 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59L GLU* 3.0 35.0 + - - +
60L ASP* 5.5 2.8 + - - -
68L ILE* 4.4 15.1 - - - +
69L PRO 4.9 3.9 + - - +
70L GLY* 4.7 3.2 + - - -
71L VAL* 4.5 1.2 - - - +
102L LYS* 6.1 1.0 - - - +
103L ALA 3.9 3.2 + - - +
104L GLU* 3.7 31.4 + - + +
132L LEU* 3.6 5.8 - - - +
135L GLY 4.1 2.1 + - - +
136L GLY* 1.3 72.1 - - - +
138L LEU* 1.3 61.9 + - - +
139L ASN* 4.2 21.6 - - - +
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Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L ILE* 4.2 7.0 - - + -
68L ILE* 4.0 25.6 - - + -
71L VAL* 4.1 10.5 - - + -
78L ILE* 4.5 3.1 - - + -
101L LEU* 3.6 27.6 - - + +
102L LYS* 3.6 1.9 - - - -
103L ALA* 2.9 41.3 + - + +
109L VAL* 4.5 6.5 - - + -
129L ILE* 4.9 4.3 - - + -
130L ALA* 4.5 11.4 - - + -
132L LEU* 3.5 28.0 - - + +
137L ARG* 1.3 75.6 + - - +
139L ASN* 1.3 61.7 + - - +
140L MET* 3.7 31.4 - - + -
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Residues in contact with ASN 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L TYR* 5.4 0.2 - - - -
58L ILE* 3.8 2.3 - - - +
59L GLU* 2.8 66.0 + - + +
100L LEU* 6.0 0.2 - - - +
101L LEU 3.3 2.0 - - - +
102L LYS* 3.3 39.6 - - + +
137L ARG* 4.2 22.0 + - - +
138L LEU* 1.3 75.0 - - - +
140L MET* 1.3 67.7 + - - +
141L GLU* 5.5 3.1 - - - +
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Residues in contact with MET 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L VAL* 4.2 7.4 - - + -
57L TYR* 3.2 15.5 - - - +
58L ILE* 3.6 28.7 - - + -
78L ILE* 3.7 16.6 - - + -
82L LEU* 4.3 11.9 - - - -
99L LEU 3.9 0.3 - - - +
100L LEU* 3.6 2.6 - - - +
101L LEU* 2.9 51.6 + - + +
114L PHE* 5.1 5.6 - - + -
129L ILE* 5.0 3.4 - - + -
138L LEU* 3.7 33.0 - - + -
139L ASN* 1.3 79.2 + - - +
141L GLU* 1.3 66.9 + - - +
142L VAL* 4.2 20.9 - - + -
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Residues in contact with GLU 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L SER 4.2 0.2 - - - +
56L VAL* 3.4 2.8 - - - -
57L TYR* 2.9 44.1 + - + +
98L THR* 4.1 19.0 - - + +
99L LEU 3.3 6.5 - - - +
100L LEU* 3.9 30.1 - - + +
139L ASN* 5.5 3.1 - - - +
140L MET* 1.3 78.4 - - - +
142L VAL* 1.3 64.7 + - - +
161L ARG* 3.2 38.8 + - - -
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Residues in contact with VAL 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L VAL* 4.4 11.9 - - + -
55L SER 3.4 5.6 - - - +
56L VAL* 3.6 24.9 - - + -
82L LEU* 3.7 21.1 - - + -
85L LEU* 5.0 0.9 - - + -
98L THR* 3.6 5.7 - - - -
99L LEU* 2.9 65.1 + - + +
114L PHE* 4.0 14.6 - - + -
140L MET* 4.2 10.3 - - - -
141L GLU* 1.3 80.1 - - - +
143L ARG* 1.3 60.9 + - - +
144L VAL* 3.6 9.4 + - + +
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Residues in contact with ARG 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L VAL* 3.2 4.0 - - - -
54L THR* 2.7 50.1 + - - +
55L SER* 2.8 27.0 + - - +
96L THR* 2.9 27.7 + - - +
97L VAL 3.7 4.5 - - - -
98L THR* 4.7 6.5 - - - +
142L VAL* 1.3 70.1 - - - +
144L VAL* 1.3 56.7 + - - +
145L ASP* 2.5 30.1 + - - +
158L ILE* 3.5 23.8 - - + +
159L LYS 5.4 0.6 - - - -
160L ASP* 2.8 47.5 + - - +
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Residues in contact with VAL 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L THR* 4.3 8.3 - - - +
52L ALA 3.3 11.0 - - - +
53L VAL* 3.7 22.7 - - + -
85L LEU* 5.1 0.4 - - + -
87L VAL* 4.2 19.7 - - + -
89L PHE* 3.5 29.2 - - + -
96L THR* 3.3 2.4 - - - -
97L VAL* 2.9 41.8 + - + +
99L LEU* 4.2 23.6 - - + -
142L VAL* 4.2 9.6 - - + +
143L ARG* 1.3 74.3 - - - +
145L ASP* 1.3 62.0 + - - +
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Residues in contact with ASP 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L THR* 3.4 2.3 - - - -
52L ALA 2.8 34.6 + - - -
54L THR* 3.1 30.2 + - + +
89L PHE* 4.5 2.5 - - - -
95L GLN* 3.3 7.1 - - - +
96L THR* 3.2 19.3 - - - +
143L ARG* 2.5 44.1 + - - +
144L VAL* 1.3 73.2 - - - +
146L ARG* 1.3 65.3 + - - +
158L ILE* 4.0 1.9 - - - +
171L PHE* 3.3 9.8 - - + -
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Residues in contact with ARG 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L PRO* 5.3 9.0 - - + -
50L GLY 3.3 19.1 - - - +
51L THR* 4.3 7.1 - - - +
89L PHE* 3.4 40.2 + - + +
92L PRO* 2.7 43.4 + - - +
93L SER 4.0 0.4 - - - -
94L LEU* 3.1 29.2 + - - +
95L GLN* 3.0 33.4 + - - +
145L ASP* 1.3 78.2 - - - +
147L GLY* 1.3 62.9 + - - +
171L PHE* 3.8 4.0 - - - -
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Residues in contact with GLY 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L PRO* 3.7 0.7 - - - +
50L GLY 2.9 32.4 + - - +
146L ARG* 1.3 77.9 - - - +
148L VAL* 1.3 65.1 + - - +
171L PHE* 3.3 22.3 - - - +
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Residues in contact with VAL 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K GLU* 6.2 2.7 - - - +
46L SER 3.5 12.6 - - - +
47L SER* 3.8 18.2 - - - +
48L ILE 3.8 3.8 - - - +
49L PRO* 3.7 23.3 - - + -
147L GLY* 1.3 80.1 - - - +
149L GLY* 1.3 68.9 + - - +
150L TYR 3.5 1.4 + - - -
151L VAL* 4.4 7.3 - - - +
171L PHE* 3.5 15.1 - - - +
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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